Boutique hotels in Thousand Islands

Find and book unique boutique hotels on Airbnb

Top-rated boutique hotels in Thousand Islands

Guests agree: these boutique hotels are highly rated for location, cleanliness, and more.

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Guest favorite

A spacious sleeping area is enhanced by a wooden ceiling, creating an inviting ambiance. Large glass doors open to a balcony, allowing natural light to fill the room. A bedside table holds a potted plant, and a soft area rug complements the flooring.

Hotel room in Clayton

4.94 out of 5 average rating, 117 reviews

Island Bay Waterfront Captains Suite

Our one of a kind location is nested right on the edge of the Village of historic Clayton, with our upstairs studio style suite overlooking our waterfront lawn and dock area, unique with great views and centrally located right in the heart of the 1000 islands area. New from top to bottom with all amenities and private balcony with dockage right in front available, a boaters dream! King size bedroom with Full kitchenette with all the essentials with full 2 couch living area with modern amenities!

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Guest favorite

A spacious bedroom features a large, neutral-toned bed and matching light wood nightstands. A decorative woven wall piece is positioned above the bed, with a soft area rug delineating the space. Natural light fills the room, aided by minimal window coverings.

Hotel room in Clayton

4.86 out of 5 average rating, 21 reviews

Island Bayside "Getaway Grotto" room

Our ”Fisherman’s Grotto” unit is right on the edge of the Village of historic Clayton, our downstairs unit overlooks our waterfront lawn and dock, unique with great views and located right in the heart of the 1000 islands area. New from top to bottom with all amenities, Smart tv, WiFi, heated towel rack,deck and patio, dockage right in front available for extra charge, a boaters dream! Super comfortable King size bed with all the essentials, enjoy a hot Keurig coffee as well as microwave/fridge

LocationFamilyCleanliness

The cozy bedroom features a queen-sized bed with a quilted gray coverlet. A wooden cabinet and coffee maker are positioned nearby. The room is illuminated by two table lamps on either side. A large area rug with floral patterns covers the dark wooden floor.

Hotel room in Gananoque

4.92 out of 5 average rating, 38 reviews

The Frederick Suite – Stonewater Manor B&B

Welcome to the Frederick Suite at the Stonewater Manor B&B. We are located 2 minutes from the Gananoque Boat Lines Thousand Islands Tours dock, the Arthur Child and Antique Boat Museums, the beach and Joel Stone Park and the 1000 Islands Playhouse. Our Frederick Suite is a cozy room that has good views of the Gananoque harbour and St. Lawrence River. This season, as a more Covid friendly option, we are offering continental breakfasts served to your room, included in the rate for your stay.

LocationBreakfastBeach

Guest favorite

A well-lit room features a large window with a view of greenery, complemented by a wooden ceiling. A compact kitchenette is equipped with a coffee maker and a small refrigerator. A comfortable chair is positioned near the window, and a cozy bed adds to the inviting space.

Hotel room in Clayton

4.9 out of 5 average rating, 113 reviews

Island Bay Waterfront -River View Room

Welcome to the Island Bay stays! Right on the edge of Historic Clayton NY, enjoy our super newly renovated waterfront “Aparthotel” style stay! Our elevated well insulted rooms and suite apartments have all the newest amenities to keep you connected and even better yet, disconnecting and relaxing to take in the 1000 islands by land or boat! Centrally located, less than a 10 min walk to downtown, Dockage available, with boat ramp and Clayton Marina and boat rentals right across the way!

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Guest favorite

A modern hotel suite features a spacious bed flanked by soft lighting. A 75-inch television is mounted on the wall across from the bed, with a sleek entertainment console below. A wall-mounted electric fireplace adds warmth, and a window offers natural light with a view.

Hotel room in Prince Edward

4.94 out of 5 average rating, 16 reviews

Cribs on Main-Picton Hotel - Suite 7

Suite 7 boasts 447 sq ft featuring a king bed, radiant floor heating, ambient fireplace, walk-in shower with a window open to the bedroom (with a privacy blind), a separate water closet, work station, a 75" smart tv and a mini-bar. Room 7 is "barrier friendly," offering a lift from the ground to the second floor and accessibility features throughout. These include wider-than-standard doors, a curbless shower, a chair-height vanity, a slide-in shower, and an available shower stool.

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Top guest favorite

The modern kitchen showcases light blue cabinetry with gold hardware and a white countertop. A stylish sink is placed beneath a decorative light fixture, accompanied by a countertop blender, kettle, and coffee maker. Above, a piece of wall art adds a touch of color.

Hotel room in Prince Edward

4.95 out of 5 average rating, 119 reviews

Beautifully designed suite on Wellington Main ST.

This stylish studio is close to all the must-see destinations in PEC! Steps away from the best restaurants and shopping in Wellington, just a short walk to the beach or Millennium trail. This beautiful suite comes equipped with a full kitchen and laundry, spacious private deck overlooking Main Street and is right above the Creekside Cafe. Our small boutique hotel has two guests suites so please inquire if you require more space. STA licence # ST-2021-0229

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Superhost

A spacious king-sized bed is centered in the room, adorned with soft linens and decorative pillows. Nightstands with lamps are positioned on either side. Art featuring trees and coastal scenery decorates the walls, while a small fireplace adds warmth and character.

Hotel room in Wolfe Island

4.71 out of 5 average rating, 24 reviews

Room 3 - Waterview King Room

Room 3 includes a king-sized bed, a private ensuite bathroom, a mini-fridge, a coffee maker, and a microwave. Guests can enjoy views of the St. Lawrence River and downtown Kingston, 5 km across the water. At night, the city lights of Kingston create a beautiful illuminated scene. Additionally, guests get free parking and complimentary Wi-Fi. Please note that none of our hotel rooms have a TV; however, guests can stream content on their devices.

LocationValueRiver

Guest favorite

A spacious room features a king-sized bed with soft linens. Natural light floods through three windows with curtains. A cozy seating area includes two chairs and a small table. A mini-fridge and coffee maker are provided, alongside a stylish upholstered couch.

Hotel room in Wolfe Island

4.85 out of 5 average rating, 27 reviews

Room 2 - Waterview King Bed

Room 2 includes a king-sized bed, a private ensuite bathroom, a mini-fridge, and a coffee maker. Guests can enjoy views of the St. Lawrence River and downtown Kingston, 5 km across the water. At night, the city lights of Kingston create a beautiful illuminated scene. Additionally, guests get free parking and complimentary Wi-Fi. Please note that none of our hotel rooms have a TV; however, guests are welcome to stream content on their devices.

LocationFamilyGetting around

Guest favorite

A spacious bedroom features a classic wooden sleigh bed covered with a soft beige duvet. Natural light streams through large windows adorned with floral curtains, highlighting a decorative dresser with floral arrangements. A cozy seating area includes an antique chair on a patterned rug.

Hotel room in Gananoque

4.89 out of 5 average rating, 53 reviews

The Garden Room - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The Garden Room is light and spacious and features a luxurious king size bed, ensuite bathroom with jet tub and walk-in shower, and private entrance onto the backyard deck.

ValueLocationBiking

Superhost

A comfortable sleeping area is presented with a spacious bed dressed in soft white linens. Two light-colored nightstands are positioned on either side, each featuring a lamp. A serene painting of sailboats is hung above the bed, offering a calming visual element.

Hotel room in Wolfe Island

4.55 out of 5 average rating, 20 reviews

Room 9 - Economy Room

Room 9 is a small yet economical and comfortable option. While it offers a roof view, guests are welcome to enjoy the shared spaces within our hotel. This basic room is ideal for weary travelers or budget-conscious guests. It includes a private ensuite bathroom and a mini fridge. Guests get free parking and complimentary Wi-Fi. Please note: None of our hotel rooms have a TV, but guests are welcome to stream content on their devices.

LocationValueLong stay

Guest favorite

Hotel room in Wolfe Island

4.89 out of 5 average rating, 28 reviews

Room 10 - Waterview Ground Floor

Room 10 is spacious and offers a spectacular view of the St. Lawrence River. It is conveniently located on the hotel's main level, right next to the guest entrance. This room features a queen bed, single bed, and sofa bed. Room 10 has a mini-fridge, and a microwave. Guests enjoy free parking and complimentary Wi-Fi. Please note: None of our hotel rooms have a TV, but guests are welcome to stream content on their personal devices.

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Superhost

A compact room features a double bed adorned with soft linens and a blue accent pillow. Wall-mounted lamps are positioned beside the bed, and a colorful artwork is displayed above. Natural light enters through a window, and wooden hooks are mounted on the wall.

Hotel room in Wolfe Island

4.63 out of 5 average rating, 16 reviews

Room 8 - Economy Room

Discover comfort and value in Room 8, our compact, basic economy hotel room designed for budget-conscious travelers. This practical space features a cozy double bed and a private ensuite bathroom for your convenience. Stay connected with complimentary Wi-Fi throughout your stay and take advantage of free parking onsite. PLEASE NOTE: None of our hotel rooms have a TV, but guests are welcome to stream content on their devices.

LocationValueCleanliness