Last year we took our kids, 9, 7, and 3 at the time, to Mammoth Cave in Kentucky. We did 3 separate tours and the ranger's that run the tour did a really good job of explaining the history of the caves. Very good/fun/educational and we'd like to go back someday.
Sometimes we just happen to accidentally run into an educational opportunity. Last fall we took the kids to a local Halloween camp that's only 1 hour away and on our way leaving the park we saw an air/space museum located across from the exit. It was a spontaneous stop but very educational.
Last year we stayed at our favorite Yogi Bear on Lake Michigan and took a day trip down to Muskegon to the USS SILVERSIDES. It's a WWII submarine that's docked but they still give guided tours. My boys still talk about this and have their souvenir posters stuck on their walls.
Depending on how far you want to drive, Mackinaw Island (between MI upper and lower peninsulas) is wonderful. You have to take a ferry out to it and motorized vehicles are prohibited. 2 years ago we took a horse drawn tour that stopped at the old fort. We even visited the blacksmith where the workers wear period appropriate clothing and show how they lived back then.