What regulations are in place for ultralight vehicles flying over US national parks?
The use of mechanized items, which UAS, ultralights and other aircraft are considered are prohibited from Congressionally Designated Wilderness areas.

That designation does not appear on a sectional chart, but can be queried from the supervisor for the park or forest.  As far as I know, overflights, particularly those by manned aircraft are not prohibited, but launch, recovery or operation from the wilderness area is prohibited.