the buses are excellent. Use google maps to help you. The Driehaus museum is walkable from The John Hancock stop, and should be a pleasant walk. BTW consider eating lunch at the restaurant that is just one floor below the top of the Hancock building - get a great, uncrowded view of the place, for about the same price you would take to go to the top. Or just get a drink.
The Cultural Center near the Millennium Gate (Jelly Bean) is also a must see. I would go to that over the Clarke and Glessner houses if you have limited time.