Secret of the Incas.
Though seriously, Temple of Doom is my favorite, while the other two are tied. Really depends on my mood, though more often than not I prefer Crusade, primarily because of SeanConnery and Julian Glover.
Now what about the scores? In that case Crusade takes the cake. You can’t go wrong with the Grail theme, the “wise old man” theme, the Nazi march, the Nazi march, and the stereotypical Venetian music.