Having just re-watched all four films, my personal ranking would be RAIDERS, followed behind by LAST CRUSADE, KINGDOM OF THE CRYSTAL SKULL, and TEMPLE OF DOOM.
My reasoning:
RAIDERS: Still (more or less) the perfect action film. A few awkward moments, but the pacing, urgency, and tone are all spot-on. The opening scene by itself is worth the price of admission. The ultimate mix of darkness, mystery, action. Best villains of the whole series. Not one but two great ending scenes. So iconic that most of the sequels were just trying to copy it.
LAST CRUSADE: A fun adventure, but the sentimental, late '80s Spielberg is in charge now. Safe and campy compared to the previous two films. Indy's father is a fun character, but he basically exists to emasculate and humiliate Indy through the whole film. Far too much slapstick, and the lamest, blandest villain of all (Walter Donovan). That being said, while the Grail hunt doesn't have the urgency of the Ark, it's still a fun ride with some cool lore.
CRYSTAL SKULL: Better than I remembered it, but still feels like a bunch of RAIDERS-themed set-pieces loosely tied together. Doesn't do a good job of explaining the goals of the characters, where they're going, or why they're doing it. Allegiances shift for no reason (Indy doesn't mind helping the Soviets find the lost city for half the film??). Way too many extraneous characters in Indy's "party" - including Shia LaBeouf. Villain is interesting but doesn't get to do anything villainous, so her horrific death doesn't feel earned. They got John Williams back but he didn't do anything interesting - no cool new themes. I was okay with the "Chariots of the Gods" theme until they just came out and put a CGI alien and UFO right on the screen. A little restraint could have been used there.
TEMPLE OF DOOM: I'll give it credit for NOT trying to be RAIDERS PART II, but that's the best thing I can praise it for. At least it's still got the gritty edge. A side story with no stakes, either to the characters or the world. Claustrophobic. Everyone except Indy is grating and obnoxious. Scenes drag on much longer than they should - you can feel Spielberg spinning the wheels because there's no driving force propelling the story forward. Worst macguffin of the whole series.