I voted Lt. Surge out of my top 3 out of my biased love of all things lightning-based. Plus, in the original Red/Blue, it was actually possible to kill one of his pokemon with a level 5 Diglet.
My other choices would be
Koga, becuase 1: he fought Tacticaly, using poison and evasion. Asshole-ish, but smart. I respect that. 2: He's been the ONLY poison Gym Leader. Why has there never been another poison Gym Leader?
Sabrina. Tough to get to, and tough to fight. In Gen 1, all ghost types were half poison, and all bugs were weak at this point, so type-wise, you're f***ed. In following gens, she overcame the type issue by just getting better pokemon.
Honorable mention to Giovanni.