We spent a week in Chicago last summer and went to the Museum of Science and Industry, the Field Museum, the Alder Planetarium and Shedd Aquarium.
I'm sorry to continue the argument, but the museum campus includes all of the above except the Museum of Science and Industry.
Before we left, I read many, many on-line reviews that suggested arriving to Shedd early! Apparently it gets very busy througout the day. I insisted we get there when it opened, and my husband laughed at me because we arrived about 30 minutes after it opened, and there was a very short line (about 10 people in front of us). The kids (3 1/2 and 6 years old) loved it! We stayed about 3 or 4 hours. As we were leaving we noticed that the line was out the door ... and down the steps and down the street. We overheard someone about halfway through the line say, "I think the wait is only about 45 minutes at this point." Wow! I highly recommend doing Shedd first! And getting there when it opens or shortly thereafter.
Because we were in town for a week and wanted to go to several museums, we did buy the Chicago CityPass, which included tickets to a couple of shows. The kids enjoyed the 4D show (it was Ice Age). We went to the dolphin show, which was mostly educational and not very entertaining (compared to Sea World). Might be more intersting for a 9 year old. We also had tickets to see the jellyfish (total waste of time!).
Hope that helps!