
Boutique hotels in Thousand Islands
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Top-rated boutique hotels in Thousand Islands
Guests agree: These boutique hotels are highly rated for location, cleanliness and more.

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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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
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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.
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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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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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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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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.
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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.
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Biglake Stay: Scene 1
Stylish, private and centrally located hotel style suite in the heart of Wellington. Kitchenette and sitting room in a shared lobby. Steps to some of the best restaurants, bars and cafes in the County. The perfect launch pad for your visit to the County, the suite has a bright spa-like ensuite and luxuriously comfortable Queen bed. The perfect ensuite Queen room to retreat to after a day visiting the amazing PEC wineries, shops and beaches.
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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.
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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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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.
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Popular amenities for Thousand Islands boutique hotels
Family-friendly boutique hotels

Biglake Stay: Scene 2
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The Pine Street Inn - Room 1
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The Pine Street Inn - Room 2

The Pine Street Inn - Room 5

The Pine Street Inn - Room 4

The Pine Street Inn - Room 6

The Pine Street Inn - Room 3

The Peninsula Room - Chrysler House Heritage Inn
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Other boutique hotel holiday rentals

Room 1 - Waterview Queen Room
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Room 9 - Economy Room
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Room 7 - Standard Queen Room
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Room 4 - Waterview Queen Room
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Room 5 - Standard Queen Room
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Cribs on Main-Picton Hotel - Suite 2
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Cribs on Main- Picton Hotel - Suite 1
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Cribs on Main-Picton Hotel - Suite 3
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