K.J.
I have done the City Pass twice with out-of-town family and friends and we went to all the museums and John Hancock. If I were to do it again I'd do Sears (Willis) Tower, since they have added the glass-floored deck where you can stand and look straight down below you...cool!!
It might be more cost effective to get a hotel near O'Hare and then take the El into the city. You can get unlimited visitor passes for pretty cheap. The Marriott Suites O'Hare is really nice, not too pricey, has free parking for guests, and is RIGHT next to the Rosemont stop of the Blue Line train. Yes, it'd be about a 40 min ride into the city, but if cost savings is a priority, this is a good way to do it. When you get a hotel in the city, you have to pay for daily parking--usually an extra $30/day or so.