I'm going to unleash a big time hot-take, but here's another boss I think is, if not best, then really good:
Petrel Heartgold/Soulsilver, Koffing Level 30 X5, Weezing Level 32.
... Hear me out here. Is this an epic battle, going up against the best Johto has to offer? No. Is it a thrilling conclusion to an evil team that's throwing everything it has at you? No. This battle isn't any of those. What it is is hilarious.
Consider your average evil team. Many of its grunts and lower-level employees will have common mons all over the place: your Raticates, your Grimers, if they're lucky a Muk or an Arbok. The higher-level members are the ones with unique mons. Ariana, for instance, has Murkrow, Arbok and Vileplume.
Thus, Petrel's choice sticks out like a sore thumb. Then you look at the moves. And you realize every single one of his Pokemon have an explosive move.
It feels like a deliberate choice by Game Freak. And in story, of COURSE the evil team is going to deploy six Pokemon that can and will explode in your face. They're an evil team! What do they care about morals or good Pokemon?
So, Petrel. I salute you, you glorious troll you.