Looks like the Chicago Historical Society tours start in June, but here's a website that lists a lot of different tours.
http://www.frommers.com/destinations/chicago/0006010019.html
The link JoefromChicago gave, Virtual Tours, was very complete for tours, I think.. (or was that Timber's link, geez, lot to learn).
I gave a boat tours from Navy pier list awhile ago, but who knows on what page - easier to just look it up again.
I suppose we should be compiling a links list/recommended places list before this thread gets to be a zillion pages.