This is tough actually, due to what we know Gregor is capable of later. It's easy for people who haven't read the books to go ahead and brush off Gregor and say that Drogo would totally destroy him, but as the rest of us know, Gregor is a tough motherfucker.
His fight with the Red Viper was intense. He doesn't go down easy. As we saw when Drogo's blood rider went up against Jorah, they apparently haven't had much experience with fully armored opponents. So while Drogo might be one of the world's finest killers, it's hard to say what he would do against a MASSIVE fully armored and skilled opponent like Gregor one on one.
I really want to say Drogo's speed and raw talent would make mince meat out of Gregor, so I'm going to go with Drogo.