Jim:
My wife, daughter and I spend 2 weeks every summer cruising the Thousand Islands. We use the ramp at Keewaydin State Park near Alexandria Bay and use their transient docks as our home port. We store the boat/trailer in a lot behind the swimming pool for the entire time, without a charge. However, we are paying for the transient dockage and therefore have a pass to the park. Another idea may be to buy a NY Empire pass for $65, which gives you unlimited access to all NY State Parks. This may allow you to park your truck/trailer at the park for a reasonable cost.
Our favorite places to visit are Clayton and the antique boat museum, Boldt Castle, Alexandria Bay (the docks are the place to be on the weekends), Kingston ON and a nicely restored mid 1800's village called Upper Canada Village in Morrisburg ON. There are also a number of Canadian Island Parks that you can overnight on. We haven't cruised the Rideau yet, but other boaters on the dock at Keewaydin have and said to budget at least 2 weeks to do so. Some have done it in 1 week but were very rushed. I hope this helps. Have a great trip and maybe we will see you there.
Rodney