The Thousand Islands would be my choice. Been to the other places and this seems to be the best. Alex Bay offers a lot to do- tours to Boldt Castle, and others like the one on Dark Island. Uncle Sam, Empire tours and others offer boat tours departing from either the Bay or Clayton. Most coincide with a tour of Boldt.
Clayton is only 11 miles down Rt. 12 and has my favorite attraction...The Antique Boat Museum...In Clayton it is the largest freshwater boating museum in the world. Their collection are facilities are simply the best I have ever seen at a boating museum. They offer rides on a HackerCraft and St. Lawrence skiffs. If you can make it, try to get to the Annual boat show August 5-6-7.
I have much more info if needed...let me know. Brad.