Pinky is the Genius
The main gist of this series is this: Brain pitches world-domination plan to Pinky, Pinky gives him some advice on the plan, the Brain ignores it, the Brain's plan fails, and Pinky's previous statement regarding the plan proves to be correct. There was also an incident in which the Brain entered into a game show, and he answers every question correctly, but he was ultimately stumped on the final question. Shockingly, Pinky was the one who ultimately answered the question correctly, and it's also shown that Pinky can read, whereas the Brain can barely write his own name.
There was also an episode in which the Brain hooked Pinky to a machine that was designed to make him smarter. What's odd though is that Pinky's personality was still intact, and that he ultimately found an error in the machine's calculations. He rearranged the machine's wiring, and the machine ultimately reveals that the Brain himself was the reason that his plans always failed.
The other thing to point out is that in the theme song for the series, it never specified who was the genius and who was the insane one; you only had to infer from their brain cases. There's also the fact that Pinky's name comes first on the title screen, and the Brain's comes next.