There are some interesting histories of the islands, including connections to Napoleon and his officers.

http://www.thousandislandslife.com/BackIssues/Archive/tabid/393/articleType/ArticleView/articleId/520/Cape-Vincents-French-Connection.aspx

The 1000 Island region offers some spectacular natural beauty.
I live in Upstate NY and my family had a cottage near Kingston for several generations. Although we sold it some years ago I still miss it.
Toronto is at the far western end of Lake Ontario and the 1000 Islands begin at the far eastern end of the Lake. Probably about a 3 hour drive from Toronto.
If you can swing it, I'd start in Kingston and head up the river from there. Definitely plan a boat tour. I have one booked for next Sunday with the Kingston 1000 Island Boat Cruise Co. The boat tours get you up close and personal with many islands and you get to sense the gracious, bygone area that was. Most tour boats (not sure about the one I'm on) stop at Boldt Castle a beautiful castle built as a tribute to one man's love for his wife. It's a little tour-istry, but it's worth a stop.
Besides Kingston, by far the biggest city in the area, other nice towns include Gananoque (Canadian side), Cape Vincent NY, Clayton NY and Alexandria Bay (A-Bay) NY. A-Bay is the most tourist oriented town in the area. Although it's very "campy" it's worth a stop, especially if you want to take a boat tour starting in the heart of the Islands. Uncle Sam Boat Tours runs several boats out of A-Bay and all offer unlimited layovers at Boldt Castle which is only about a 1/2 mile across the river from Alex Bay.
The entire area is fairly compact and the drive from Kingston, Ontario, to Alex Bay NY is probably less than an hour.

Have not been. A well traveled friend of mine called it "the best kept secret in America".

Enjoy!

In addition to the traditional 1000 islands "area" The whole Bay of Quinte / Prince Edward County area is stunning - I'd highly recommend a night in that area- there's really great food and even wineries.

And take one of the tourist cruises of the 1000 islands.. They really are cool.

I've never been, but I know someone whose family has a house there. They are loaded (for generations) and could have a house anywhere they want. The pictures are gorgeous.

We are going to Toronto in a couple weeks and we're thinking of making 2-3 day stop in Thousand Islands. If you've been there, or are aware of the place, please share your thoughts.

Thanks!