If you take I-90, after the long drive across eastern South Dakota and Minnesota, the kids are probably going to be ready for a stop. I would suggest a stop at Wisconsin Dells. Although it has become overly commercialized with every kind of entertainment you can imagine, it's still a great place for kids. You name it, they have it. The original attraction, boat trips through the Dells Of The Wisconsin River is still there. I would suggest the Upper Dells Trip because the boat makes a couple of stops and you get to walk through some very deep ravines that run in to the river. There are a couple of high-dollar hotels that have their own huge, indoor waterparks. We prefer a little less hustle and bustle and usually stay at a nice place on Lake Delton called Sunset Bay Resort. It's in a wooded, secluded area but still very close to the activity of Wisconsin Dells. They have a little sand beach and you can rent canoes and peddle boats.
A great place to eat in Wisconsin Dells is Ishnala. It's on the pricey side but the food is wonderful and the kids would enjoy the Native American decor. http://www.ishnala.com/
Just south of Wisconsin Dells at Baraboo is The Circus World Museum. They have some circus acts, animals and a wonderful display of old circus wagons. When we took our daughter there when she was 5 or 6, she got to take a ride on an elephant and she still remembers it fondly 26 years later.
If you happen to have some time when you're in the Sioux Falls, SD area, there's a very nice city park called Falls Park where the falls that gave the city it's name are located. The kids would get a kick out it.
Another stop the kids might get a kick out of is the Corn Palace in Mitchell, SD. It's a castle-like structure which is decorated with colored ears of corn. They redo it each year and this has been going on for over a hundred years. It too is one of the things I've always remebered from a visit to South Dakota more than 60 years ago. It would only take a hour or less.