Besides the fact Raiders is more famous, how is it better than any of the other two? Nobody should act like its superiority is obvious at all.
I think my assertion comes from the fact that I have been defending Raiders for so long against people who have seen Last Crusade a dozen times but Raiders once or twice at best.
Bear in mind that I enjoy all three movies and think that Last Crusade is a perfect end to the Indy saga, part of the reason why I'm still annoyed that they're making a fourth film. But it has to be said, Last Crusade is much more cartoonish than Raiders. I know that Raiders has its moments where it gets a little silly (i.e. the Nazi monkey, "bad dates") but for the most part, it plays it straight without being any less fun. Temple of Doom is by far the most ridiculous, there's no denying that, though I still really enjoy it. Last Crusade splits the difference. It plays it much straighter than Temple of Doom but the characters are still more caricatures than they were in Raiders, with lots of winks and nods along the way. Yes, the father-son aspect of Last Crusade does provide an emotional thru-line that the other two didn't have and a lot of the fun of the movie comes from that. But I feel that Last Crusade, as much as I enjoy it, is a borderline pastiche of Raiders.
Take the character of Marcus Brody. In Raiders, he is a straightforward curator. Not a particularly interesting character, that's true. But in Last Crusade, he is inexplicably turned into a buffoonish comic relief who "got lost in his own museum." There is zero evidence of that in Raiders and not particularly necessary in LC as Henry Sr. was already portrayed as out of his element in Indy's world. We don't need two characters filling the same function at different times (and occasionally, the same time). Sallah, who was mild comic relief in Raiders, was much more over the top in Last Crusade. Even Indy himself was at his silliest in that one scene where he's faking a Scottish accent to get into the castle; that in particular was so out of character for him. Then there's the scene where Indy meets Hitler and gets his autograph. Yeah, these are all funny moments and they work well within the story but they border on self-parody. If the story itself wasn't as well-crafted or the action sequences as spectacular, no one (myself included) would be as forgiving of it.
Again, I'm not really knocking the film; all these gripes are completely insignificant when I'm watching the film but at the same time, they're also minor points against it when comparing it to Raiders.