computer > Human Brain. And even if you don't agree woth this, Metagross is a combination of those two (with pokémons having souls and all), so he definitely wins.
But no, regarding just those two, I would say Alakazam, just because we don't know Metagross' IQ. In this situation, 4 things aren't necessarily better than one. All four of Metagross' brains would know the same things and would be as intelligent as one another. With an IQ of 5000, Alakazam pwns Metagross if its IQ isn't at least 5001. It would be pointless for Metagross to have more than one brain if its IQ isn't on par with Alakazam's.
I still agree with my theory. It seems very plausible.