Dude, the Field Museum sucks, honestly. I would not waste your time there. The Museum of Science and Industry has a ton of cool stuff. The Alder Planetarium is way better also and right next to the Museum of Science and Industry.
Shedd Aquarium is ok I guess. I went before they opened the penguin exhibit so I was upset about that.
As for Zoo's: Lincoln Park Zoo is free but a bitch to find parkin. Pretty good zoo but seems "empty" to me. Brookfield Zoo is better but you have to pay to get in. It's pretty big and the food sucks.
I've never really liked Wriggleyville. It's mostly bars and yuppies. Maybe it never tickled my pickle because I don't drink alcohol.
And I would only consider going to Navy Pier if you are planning on taking a boat ride around the lake front. Other than that it's mostly jus' a place with a few places to eat, a small exhibit of stained glass art and a "upscale" flea market.
Oh, and keep in mind as you begin to look at maps and expressways of the Chicago-area that the I-290 (Eisenhower EXP) is a reduced to a two-lane expressway. It is pretty much undriveable. If you are in the center of the city, I would use Cermak (22nd Street) as an alternative. It runs parallel to I-290 and is a safer street that Roosevelt (12th Street).
since you are going to be busy during the day then i really suggest checkng out Blue Man Group in the evening. Great Show!!
as for food.....Portillo's for a Chicago style hot dog and Lou Malnati's for some deep dish pizza! dont forget to find some place that sells itallian beef and gyro's. chicago has some of the best food of any city of this country.