dmjr,
I enjoy going from island to island and I'll ditto what Lucky2Behere said: the best time to go is early morning, preferably weekdays but early on the weekends is okay, too (not quite as peaceful as the weekdays but still empy enough if you go early). Sunday evenings are usually glorious; most of the boaters have gone home and the loons come back out. Winnipesaukee is a great place to kayak. Enjoy and I'll be watching for you.