Pete- The following website might be of interest for information on kayaking in the 1000 islands region www3.sympatico.ca/helmer/leif/gopaddln/contact.htm. I did a week long sailboat cruise in that area a few years back and always thought it would be an interesting place to go in a kayak. I have no experience (or association) with the individual running the website. There seems to be some useful information about different kayak routes on the website. Hope it is helpful.

Regards, WesT