It's been a few years, but I think The Last Crusade is the best of the four because of the wide range of action sequences we see with beginning, middle, and ends. The use of boats in Venice, an old medieval castle, planes, a desert, sewers... There isn't a repeat sequence, something that I think has really hurt the Marvel and Fast & Furious movies. They all seem like the same sequence.
Add to that, I think Indiana really hits the mark from beginning to end, the Sean Connery character is the best of all the sidekicks in the movie, and I think the use of the supernatural at the end is far scarier and more interesting than what we see in Raiders.
I actually REALLY enjoy all of the first three, but Last Crusade is always the one I'll return to.