Re: best time for cruising the 1000 islands?
The crowds are hardly ever all that bad. I'd stay away from Alex Bay on July 4th, or during Pirate Days. Check the schedule for the Antique Boat Museum in Clayton. The weekend of the boat show is super busy, but it's a neat experience, and the parade is best seen from the water. But starting your trip the Tuesday after Labor Day will definitely miss all the crowds and the water will be still as warm as it ever is.