Ph, have you done the Museum of Science and Industry down in Hyde Park? That's a must, IMO. Hyde Park is an easy bus ride from downtown, or you can take the Metra commuter rail which leaves from under Millenium Park.
That said, Hyde Park is enough of a trip that it's worth making it a half-day or full-day trip. Other than the Museum of Science and Industry, you can also check out Obama's house, though that requires a longer walk than I'd probably want to make with kids. If it helps, R. Kelly's high school is between the Museum and the Obama house.
As for the boat tours, IMO the only ones worth taking are the architecture tours that go along the river. Getting out on the lake and seeing the skyline is nice, but the river tours are more interesting.
Probably best to wait for JuiceCrewAllStar to chime in here. I'm 2 years removed from Chicago these days.