Kingston is a great town. Lots to do and see. Confederation basin is the place to stay. Right downtown. They don't have fuel or pump out facilities, though. They will take reservations via website only, and only if you register more than 48 hours in advance. You'll likely be able to get in there even without a reservation. There always seems to be space available.
I can definitely recommend Clayton. It's a nice town with several marinas, and a nice municipal dock. There's power, water and pretty decent showers and heads. The antique boat museum is an interesting diversion, and there are several nice shops. Bella's and the Wooden Boat Brewery are both very good. Also, if you need any work done, the mechanics at French Bay Marina are very good. There is an unbelievable wealth of spare parts at French Creek Marina. An older gentleman by the name of Wilburt has built an incredible empire there. If he doesn't have what you need, nobody does.
Alexandria Bay is a bit more crass, a bit more party town. There are lots of places to get loud and drunk. I don't recall ever having had a great meal there, so I can't make any recommendations in that department. Riveredge resort has nice docks, a pool, bar, restaurant, power and water, but is a bit pricey.
A big part of the draw for me is the natural beauty of the area. I get lots of joy from just weaving around the islands. Make sure you have good charts. There are lots of rocks and shoals that aren't marked.
The Lake Fleet, Navy and Admiralty islands are beautiful. There are lots of Canadian national park islands with docks and heads, but little else. No power or water. They're inexpensive and fill up quickly. If you're into boat camping, they're worth a look.
You'll want to see Boldt Castle, for sure. I've also heard good things about Singer Castle on Dark Island, but haven't been, myself.
Cape Vincent is a town I remember fondly, but I haven't been there in a long time, so I'm not sure how it looks these days. Same for Gananoque.
Have a great trip! Let me know if you have any other questions.