I know how to restore hit points with Stimpaks but Cass is fully healed and still limping around like she has an injured leg. How do I hea that?

You click on the companion and select "talk to ". A choice wheel will come up. Select heal (I think it is on the right lower quadrant of the wheel). It should show # of stimpaks and the health of the character.

Edit: Sorry. Reread your question and it looks like you already did this.

When Boone limps I just heal him normally and he comes back to standing straight.

I had a similar issue. I think it clears up on its own the next time you enter combat.