You will see all kinds of hotels along I-90 in Rapid City.
Exit 61- LaQuinta, Marriott
Exit 59- Quality Inn, Ramada, Holiday Inn, Motel 6, AmericInn, Best Western, Country Inn and Suites, etc...
Exit 58- Red Roof Inn, Grandstay
There are also several nicer, but more expensive hotels downtown but I doubt you wanna stay in town if you're just passing through. Have a safe trip!