If you do the route along the St. Lawrence from Cape Vincent to Alex Bay, be reminded that crossing the Thousand Island Bridge back in to Canada is a harrowing experience. You have a narrow walkway, barely wide enough for your body and bike. It's scary! Well, at least I thought so.
I would go to Kingston via Gananoque, take the ferry to Wolfe Island and bike around the Island. Or...go on over to Cape Vincent via ferries and bike up to the Lighthouse or go down along the St. Lawrence river. Then return via the ferries. Have fun!