The Art Institute is awesome. I grew up in DC, so I understand your aversion to paying for museums, but it's worth it.
I can't recommend a Wendella architectural tour highly enough. To me the river tour is fine, the lake gives a nice view, but it takes a while to get through the locks.
For food, I'd skip the deep dish because its disgusting and only about 3 Chicagoans actually eat that crap. Best pizza in town (begin flame war) is Piece in Wicker Park. Spacca Napoli in Ravenswood and Reno in Logan Square are good too. Though if you're heading up to Logan Square you should probably go to Lula instead.
The best, reasonable food in the city is in the neighborhoods. The loop is great for walking around and gawking at tall buildings and shopping, but the neighborhoods are where the character is.
If anyone in your party is a vegetarian, the Green Zebra is the place to go.
The Sears Tower (Whatchoo talkin' bout, Willis?) will take forever most times of day. As any local will tell you, go up to the lounge at the top of the Hancock building, get an overpriced drink, and enjoy the view.
Oh also, if you're looking for a massage while you're there you can't go wrong with Acchaa in River North. While you're there you can check out the galleries a little bit to the west, then get a beer at The Green Door.