For me it's a very close tie between Argarok and Stallord. They are both really cool bosses, and their battles are unique in the way that Zelda has never had anything like them before. Sure, we've seen Stalfos, and we've seen dragons, but we've never fought either of them likes this.
Argarok his epicness going for him. His fight was on the very peak of City in the Sky, high above the clouds. And the only thing keeping you up was your Clawshot a couple of wobbly towers. Other then jumping onto his back and slashing him, the rest of the fight wasn't very cool. It was very easy, and it mostly consisted of swinging around to his back. Cool premise, bad execution. Still an awesome boss though.
As for Stallord, his battle was also fairly epic, and he was definitely more difficult, but I really didn't like the setting. The giant crypt/sand/pile of bones thing wasn't very practical, nor interesting. Never mind epic. I really did like the thing that they did with the chase on the Spinner. That was really fun and interesting, but the rest of the fight was a little less awesome. Still good though. Now if only they could have incorporated some of the fighting elements when you fight him in Link's Crossbow Training..
Anyway, over all it's a tie between Argarok and Stallord. I didn't really care much for the other two of these four bosses.