The subway in Chicago is called the 'El' (can't have you sounding like tourists now), but you can catch that at the airport and head to the Hancock building as your hubby said. That whole area is called the Magnificent Mile - lots of upscale stores and a mall called Watertower Place. The American Girl store is right in that area as well. But also just a couple blocks from there is Gino's East - you must go there and have a traditional Chicago pizza. It's probably a 5 minute walk from the Hancock building. There can be long waits, so I'd say to get there early-ish. And you can write on the walls - kids love it. Bring white markers. I don't think you can be in Chicago even for just a few hours without going to Gino's. You want the pan/stuffed pizza.
And then take a walk up/down Michigan Avenue. You will smell something wonderful and it's another Chicago favorite - Garrett's popcorn. There may even be a line for the most wonderful carmel corn. Mmmmm... A snack for your flight.
Across from the Hancock Bldg/Watertower Place is the actual Water Tower Building - the only building that survived the great Chicago fire. There's also a little museum adjacent to it, but like you said, it will probably be closed. Horses and buggies line up there to give people rides around the city, and if they've never done that before it might be fun for them.
It's more than a walk (or maybe a long walk) but if you keep going south down Michigan Avenue you'll cross the Chicago River and you can go to the new Milennium Park. You've probably seen pictures of the Bean sculpture. I think there is also an outdoor ice rink there that your boys may be able to skate on. Perhaps you can look up the specs on the Milennium Park website, as I haven't been skating there.
So here's what I'd do... I'd take the El downtown, depending on the time, go to Gino's and have an early pizza, take a $10 cab ride to Milennium park and skate. By the time you're done it'll be dark and if you have time the view from the Hancock building will be much better than during the day. Walk/cab Michigan Ave time permitting and I think you'll have a great evening. Be careful if you plan to take the El back to the airport because some lines stop running late at night.
Have a great trip and give Chicago a big hug for me!