In the hart of the Thousand Islands, the Antique Boat Museum in Clayton NY is a hidden gem. I haven't been there in many years but from the web site it looks like they have more now than when I was there and it was very impressive back then.

Just to the East of the Thousand Islands, Brockville is a friendly little town with a nice harbour right down town if you are looking to tie up.

Between Brockville and Cornwall, Upper Canada Village is an historic town museum. One of those places where they have everything set up the way it was 150 years ago. This one is interesting in that a lot of the buildings were brought in when the St. Lawrence river was flooded to create the Seaway. I have only been there by car and I have no idea about mooring or anchoring but Cornwall is nearby to the East where there is a marina in the middle of town. Not much else to see in Cornwall.

Old Montreal just east of the Lachine lock system is the place to go if you only have a short time in Montreal. I stopped in here several times while working on a cruise ship but never in my own boat so I'm not going to be any help with marinas.

Quebec City has a great marina right in the old town. There is a lock into the marina so there is no tide inside. I would spend at least a full day and night in the old Quebec but plan for more if you have the time.

Jon mentioned the Saguenay river and I would highly recommend it. At the mouth of the Saguenay, stop in at Tadoussac. I saw minke whales breaching right in the bay coming in here once. You can often see minkes and belugas around the mouth of the Saguenay. The Saguenay river itself is quite beautiful and worth the side trip if you have time. That is as far East as I've been by boat on the St. Lawrence but as mentioned above the maritimes offer plenty of opportunities to explore beautiful places.