Consider staying near the Mall of America (assuming that is one of the attractions you'll be visiting). There are a number of chain hotels in the area and although you're south of "the cities", you'll be fairly central for visiting attractions. (The MN Zoo, Childrens Museum, Science Museum, Como Zoo, Target Field, etc.) Another advantage is free parking. The downtown hotels generally charge extra for parking.
If you are interested in visiting downtown Minneapolis you can take the light rail from the MOA to downtown.
There's a great outdoor waterpark in Eagan, about 10 minutes from the MOA. It's less expensive and less busy then the Waterpark of America (indoor waterpark near the MOA).
Enjoy your stay!