1. RAIDERS. No contest.
Ouch!
Seriously, though... such a poll isn't even fair. As much as I enjoy all of the INDY flicks so far (though TOD more than TLC) it's clearly RAIDERS that is the untouchable of the lot. It's not only the best film of this series, I'd go so far to argue that it's the best film of its kind, period.
RAIDERS is flawless to the point where one could call it the perfect action-adventure film. So it's not only the obvious flagship of this series, it's the pinnacle of an entire genre of film.