The two best rock-related museums in the Chicago area are:
The Lizzadro Museum of Lapidary Arts in Elmhurst, IL, has rock, mineral, and gemstone exhibits, programs for children, and online activities.
Also, Dave’s Rock Shop in Evanston, IL, has a museum in the basement.
It’s not a museum, but Brookfield Zoo’s Hamill Family Play Zoo has a Nature Swap, where children can trade natural materials for rocks and other things. (Check when the Nature Swap is open before paying them a visit.)