Another unknown National Park that shouldn't be is Greenbelt NP in the Washington DC area. It is even left out of "Your Guide to the National Parks" (the Complete Guide to All National Parks). It seems like it is most unknown by our National Parks Service. Every time I'm there I am ashamed at the quality of upkeep since it is often a park where foreign visitors stay when visiting the nation's capital.
A National Monument that I enjoy for exploring lava tubes is Craters of the Moon in Idaho. Also a great dark skies location. A couple more that I like - Organ Pipe in southern AZ & Natural Bridges in UT. Not as unvisited as those linked below, but well off the beaten path.
Here is a list of the least visited places in the National Park system.
