We have stopped at most of the Lewis and Clark sites mentioned above by others. To me the best was seeing Clark's signature carved into the sandstone of Pompeys Pillar. It's the only remaining physical evidence on the landscape that the journey actually occurred. Pompey's Pillar is an easy off/easy on to I94 east of Billings, MT.

We also enjoyed a visit to
Spirit Mound, a few miles north of Vermillion, SD.

Adjacent to the Lewis & Clark Interpretive Center in Great Falls is
Giant Spring State Park. The Spring was discovered by Lewis & Clark in 1805.
A few miles south of Missoula, MT at the little town of Lolo is the site of the
Traveler's Rest encampment. Lewis & Clark stopped here both west bound and east bound. A recent archaeological dig here found evidence of the actual site of the camp.
Not a Lewis & Clark site, but
Fort Abraham Lincoln south of Bismark, ND was the last post of General George Armstrong Custer and the 7th cavalry before the battle of the Little Bighorn. Several fort buildings, including the house he lived in have been reconstructed. They have a campground with electric and dump station.