Raiders, all the way. No comparison. ToD was silly, straight up. The Last Crusade was great. I agree that Connery and Ford was a great pairing, but that shows up the rather worn plot. The Holy Grail, even by that point, had been the talking point of a great many pieces of cinema.
The reason I dug Raiders so much is because I doubt many people had ever even heard of the Ark of the Covenant prior to Raiders. Spielberg and Lucas really brought back the pulp hero with their introduction of Indiana Jones, and in no other movie did Indy come across THAT badass. He couldn't be stopped. He was smart, adventurous and he had an amazing, unique adventure in front of him. With Crusade, Indy was constantly in competition with his father over who was the smarter historian, and he just seemed way more bumbling, plus the aforementioned plot pieces I personally take a tiny bit of issue with. In my eyes, the movie stigma of the first being the best still holds true, while the third (and what should have been the last) installment follows with a close second, followed by of course ToD and then KotCS, which was a giant slap to the face to every Indy fan, ever.