Chicago is the big city that's easy with kids. It has the museums of a much harder trip, a zoo you don't pay for, and a lakefront park that runs the whole length of downtown. Kids can see a real submarine in the morning and splash in a fountain by lunch.
Two rules make the whole trip work.
The first is one big museum a day. The Shedd, the Field Museum, and the Griffin Museum of Science and Industry each take half a day or more with kids. Four hours goes fast. Parents who try to do two in one day say the same thing afterward: it was too much. The Shedd and the Field sit right next to each other, which makes it tempting. Don't. Do one in the morning, and spend the afternoon at a playground, a beach, or the hotel pool.
The second rule is no car downtown. Hotel parking is expensive, and street parking is worse. Downtown is walkable, the buses go everywhere you'll want to go, and kids under 7 ride the trains and buses free. Keep the car for day trips, or skip it completely.
Where you stay matters a lot here. Base yourself in the middle of things, in Streeterville, River North, or the Loop, and you can walk to most of the trip. Stay farther out to save money and you'll spend part of each day on the bus.
The weather is the other big factor. Late spring through early fall is the easy season. Winter is cold and windy, but if you come in November or December, the holiday lights, markets, and skating make up for it.
The sweet spot is 5 to 12. Toddlers do great too, with a smaller plan. Three or four nights is right.