Art Institute is fabulous and Navy Pier is a nice place for a walk. If the weather is nice, our kids really enjoyed just taking a water taxi from (Adams Street bridge, I think) to Navy Pier. You see so much lovely architecture that way and its much more fun than a regular cab. I think it was about $20+ dollars for all 5 of us.
I love the water taxis! My kid and I use this one
http://www.chicagowatertaxi.com/ for joyriding. It goes from Michigan Ave all the way down to China town and you can get an all day pass for $6pp.
Search online...they used to have one day a week free at the Aquarium, but I'm not sure they do anymore. I think you can still buy a pass for the Aquarium, Field Museum, and Planetarium.
Personally, I recommend looking up when the free days are and avoiding them like the plague. You'll save some money, but you'll be dealing with oceans of people. I'll never go to any museum on a free day again. You don't really get to see anything because you're too busy trying to dodge people.
You won't reget going to the Museum of Science and Industry! And a Cubs game if you can get tickets!!!
Museum of Science and Industry is one of my favorites. There is an express bus you can catch on Michigan Ave. Take time to walk around to the south side of the museum and visit Jackson park. Follow the signs to the Japanese Garden. Its heavenly.
Cubs tickets aren't really in demand right now. Check out Stubhub.com.
I'd also recommend signing up for groupon.com and livingsocial.com for Chicago. You can find some great deals!
As far as a room, I'm copying and pasting this from my reply in another Chicago thread:
When my family comes to visit they usually book with hotwire.com. For neighborhood/area choices on their map I'd suggest Magnificent Mile - Streeterville, North Michigan Avenue - Water Tower - Gold Coast and Chicago Loop - Millenium Park - Grant Park.
As stated above, these hotels all charge a ton for parking. I would not recommend staying at hotels by the airport or in the burbs. Chicago traffic stinks and it can easily turn into 3 hours or more per day in travel. "Rush hour" is really the better part of the day, and baseball games and festivals can really mess things up too. If the president comes to visit you're really up a creek. (I was recently working downtown with a couple who decided to save money by booking a room in the suburbs. The president came to town. What is usually a 45 minute drive without traffic, was being reported on the radio as being over 3 hours. They weren't happy at all.)
The other option I would recommend are some B&B's in my neighborhood.
www.twourns.com,
www.wickerparkinn.com, and (this one doesn't come with breakfast)
http://web.rubyroom.com/inn.aspx The neighborhood is fabulous, you'll be close to a lot of wonderful things, and I don't think any of them charge for parking.