To me, objectively speaking, there's no question that Crystal Skull is both the least necessary and the one of the lowest quality. The choice is easy.
I will say though, as a protracted aside, that as superbly made as Last Crusade is, its absence would make the series way less formulaic and (unnecessarily) interconnected. The original idea for the Indiana Jones movies was for it to be Lucas and Spielberg's answer to James Bond, with each adventure being self-contained and allowed to go in its own direction. If you just look at Raiders and Temple, you can see that - the two movies are unmistakably part of the same series, but there's a different tone, leading lady, structure, influence, etc. etc. When Temple got trashed for being too dark, Spielberg chickened out and just made Last Crusade a really well made rehash of Raiders, using a template that isn't colored outside of nearly enough. We get the Christian artifact, we get Marcus and Sallah, we get the Nazis, we cut to a college in New York after the prologue, etc. Things suddenly became staples of the series that didn't have to be. Spielberg made a great movie with Last Crusade, but he didn't make an original one. It's really Last Crusade's fault that so many fans treated Indy4's new 50s influences like they didn't belong, because Last Crusade helped imply that Nazis and biblical artifacts were the only "right" features of the Indy universe by being traditional. (When you only have three movies, two is a majority.) Temple of Doom only became the series' black sheep retroactively.
Of course, I consider Indy4 to be way worse of a movie than Last Crusade, and it has plenty of unneeded ties to what's come before anyway, but I can at least appreciate that the movie, like Raiders and Temple, had its own story to tell. I can list direct outside influences to the storyline and style of Raiders, Temple, and Crystal Skull. For Last Crusade, the only obvious inspiration I can think of is...Raiders of the Lost Ark. The movie's inbred. It's actually sort of interesting to think about how the series might feel if you knocked out Last Crusade and made Crystal Skull the capper to the trilogy. I wouldn't prefer it in a million years, but it would be interesting for certain reasons.