I voted for ROTLA. The Ark wiped out all the Nazis for him. He was impressed enough to close his eyes in fear, something he didn't do in the other movies. And this was supposedly power directly from God, something that must have impressed him once he found out it was true. Heck, in Crusade, he was still arrogant enough to think he could grab the grail, showing he wasn't that impressed with its power. TOD, what the stones do just isn't anywhere near that impressive, and doesn't phase him at all.
KOTCS is the runner-up, but ultimately he's just looking at technology during that finale. He doesn't see any incredible, mystical powers on display. If the final moment didn't involve a big object, it wouldn't be that impressive. It could have been the aliens jumping into a small machine and disappearing with the push of a button. He seemed to have resigned himself to the existence of aliens after being "hypmotized" by the skull, and just accepted it, without being amazed. The ending adds nothing to that other than a large-scale vehicle and special effect.