1000 Islands is my play ground........so much to see in so little distance.
That's a lot of mileage per day and a lot of fuel.
The 1000 Island range from Kingston to Brockville, or Cape Vincent to Morristown.
There are transient docks available at almost every marina on both shores.
Alex Bay has some good hotels with docking, I'm not too familiar with Clayton or Cape Vincent, but I'm sure there are places.
ABay's municipal dock is good and deep, and it's right downtown so you can eat or just wander the shops.
At the municipal dock in Clayton the dockmaster will call and arrange someone to puck you up if you need groceries, booze, or just a nice meal.
We do it a couple of times a year just to check out the restaurants.....and a couple are quite good.
On the Canadian side there are a number of islands with docking where you pay a fee and stay up to 3 days. There is nothing on the islands and you must take out what you bring in. They all do have very good outhouses.....LOL The best is Grenadier centre, it has actual toilets and running water.
As for hotels on the Canadian side, Brockville has transient docking and a couple of hotels within walking distance, but the big ones are a taxi ride from the water.
Gananoque has municipal docking and a few hotels close to the water.
A real nice place to stay is The Glen House just west of Ivy lea...good food, good rooms and docking. Just down river is The Ivy restaurant in the Ivy Lea Club, it is the best fine dining on the river and you can go in wearing anything but a bathing suit, shorts and tee shirts are the norm.
I could go one forever, but if you have some questions.....ask.
Hope you enjoy the islands