After Indy is forced from his university position, he sits at his desk and looks at two framed photographs, one of which is his father.
INDY: Brutal couple of years, huh Charlie? First Dad, then Marcus.
CHARLIE: We seem to have reached the age where life stops giving us things and starts taking them away.
It's never made clear how they died but the implication of death is plain enough.
As for the grail, the knight who guarded it said "But the grail cannot pass beyond the Great Seal. That is the boundary and the price of immortality." I took this to mean that you were immortal only so long as you didn't pass beyond the seal. Water from the grail healed Indy's father's injuries but did not make him immortal. Indy drank from the grail, but he too lost his immortality once he left the grail site.
