Our science museum rocks
http://www.smm.org/ You don't have to see the King Tut exhibit there right now (that is pretty pricey, although interesting). There is a lot of other stuff to see and do if you just get general admission tickets. The Omnitheater is also good, of course -- would recommend booking those tickets a day or two ahead of time to make sure you get the times you want if you choose to do that.
Although the museum is over in St. Paul, it is pretty easy to get to from Eden Prarie (which is south of Minneapolis, and the museum is on the south side of St. Paul).
We also really like the Minneapolis Institute of Arts.
http://www.artsmia.org/
