It's so tough to answer a question like that.
There is a lot of settlement and immigration history to be discovered in the dozens of small museums and various historic sites in eastern South Dakota.
If you're looking for general history, Pierre/Ft. Pierre may be more appropriate, given the state museums and archives there.
If you're looking for history regarding natives and the 'old west' (whether it's the gold rush or the open range days), Rapid City is definitely the best bet.
And there's really no shortage of natural beauty anywhere in the state, especially in summer. Whether it's the wetlands and waterfowl in the northeast, the hardwood forests in the extreme southeast, the Missouri breaks in the central region, the Badlands, or the high plains butte country in the northwest, you don't have to be in the Black Hills to experience beautiful scenery.