Let's compare it with another fight between to skilled swordsmen from each culture that's actually in the show.
Drogos brother, not the epitome of a warrior that Drogo is, but clearly a skilled warrior, fights ser Jorah Mormont, exile knight in full plate. It's not an entirely easy thing, but Jorah wins and does so rather abundantly.
Khal Drogo is the superior swordsman in his culture and would win if they fought on his terms. The Mountain that Rides is a superior knight and if they fought on his terms he would win. But if both fought on their own terms ser Gregor would win, simply because he has plate armour, a shield and knows how to wield them.
As we saw in the show the dothraki have no idea how to fight versus armour and I doubt Drogo could come up with a strategy in time, especially as he can't penetrate the armour with the made-for-slashing sword that he has.
Oberyn certainly made a match of it, but he knew what he was fighting and had trained especially for that sort of warfare. Drogo has not.
So: of the two colosusses of war, the Mountain that Rides would win.