Chicago for tots
As a northern suburbs mom, I can vouch for the use of strollers throughout the Chicago transit system, from Metra trains into the suburbs to the CTA (L and bus). And cabs are everywhere, unless it's pouring rain. If you're bringing you car, the Best Western close to the Loop has free overnight parking for guests. Otherwise, hotel parking is extra and it's pretty pricey. I've stayed in many hotels downtown and there really aren't any bad ones. Go to choosechicago.com for good hotel deals.
Other than the usual places you may have heard about--Millennium Park, Navy Pier, and the museum campus, which are all good and worth seeing--I would suggest a couple of neighborhood spots. Consider Andersonville, a former Swedish neighborhood. They have a children's museum and Ann Sather's is a delicious breakfast spot for families. A fun and bustling breakfast/lunch spot in the Loop is Lou Mitchell's on Jackson St. Great omelettes and coffee, and the waitresses love kids. Another fun neighborhood would be Chinatown, south of the Loop. Take the L to Wentworth Ave. and head west. Lots of fun shops and restaurants to explore.
If you are thinking about the Art Institute, the new modern wing would be interesting to your 3-year-old as well as adults. There are so many interactive exhibits and photography that it's quite a visual feast.
If your 3-year-old is a girl, American Girl Place near Water Tower is fun. The cafe encourages girls to bring their dolls and puts them in a "baby" seat. Cute.
Enjoy a water taxi ride if you come while the weather is good. It's a great way to see the city, and it's inexpensive.