It's definitely Belloq. At least Indy sees it that way. He doesn't call out to Toht when he threatens to blow up the Ark.
They're bitter rivals. They're both interested in the same woman. And the whole scene in the Cairo bar lays it out pretty plainly that Belloq is Indy's nemesis in the film. Toht is evil, but closer to Dietrich as far as importance goes.
Maybe. I don't know if there's really a "primary" villain. There's three.
There's Belloq -- essentially an "evil" version of Indiana for collaborating with the Nazis and allegorically the Vichy French before there was a Vichy French submitting to the Nazis.
Toht is pure Nazi evil. Like I said, he's cast, dressed, and made up to look like Heinrich Himmler, the main architect of the Holocaust and probably the most evil Nazi of them all. Belloq is an ******* but the worst he does is put Indy and Marion in easily-escapable situations. Toht was just about to torture and mutilate Marion with a red-hot poker because he thought it would be fun before Indy swoops back in.
Dietrich is one the same tier (the meathead German colonel who barks a lot of orders and openly advocates turning Toht loose on Marion while captive). He is notionally in charge of the whole thing.
All three of them get what is coming to them at the same time at the end in memorable fashion.
Each have their allegorical and practical contrasts to Indy and Marion.
Belloq does have the best counterpoint, though --
"We have always done the same kind of work. Our methods have not differed as much as you pretend. I am a shadowy reflection of you. But if would have taken only a nudge to make you the same as me, to push you out of the light. You know it to be true! How nice. And how ironic the timing."