It entirely depends on what you think Majora is and how you consider its power. Ganondorf's power is established and explained (well, except that it can differ a bit from game to game), but Majora's is a little more abstract.
I myself would say Majora, though. Yeah Ganondorf can only be slayed by the Master Sword, but that's not as relevant in something like this I think, because I almost look at the Master Sword as a plot device rather than a very important detail in the actual mythos. Ganondorf's immortality to anything except the Master Sword also likely derives from his possession of the Triforce of Power, which means it's essentially a direct blessing from the Goddesses.
My take on Majora is that it is a demon, or a devil. An entity of pure evil. And this makes him either a fallen god or an anti god. Because of that, I think it almost puts him on par with the Goddesses. He's probably not as powerful, but I think saying he's close is fair. And I think even if he's weaker than the Goddesses, putting him on above someone who only has some of their power also seems fair to me.
Another issue is how both are portrayed. Ganondorf in all the recent games is simply a man. Despite all his divine and/or sorcerous power, he's a man with ambitions trying to take over and rule. Even in the classic games, where Ganon is less human and is portrayed as the "King of Evil" or "Demon King", despite his amplified evil he's still only a ruler. But Majora is portrayed as the ultimate evil. The destroyer. The final evil. That kind of thing. His actual presence and role on the story is much more powerful, intimidating and malevolent. I think this shows an element of the creators' actual intentions, and that above all else is why I say Majora is the more powerful entity.
