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I'd have said Meowth if he wasn't his own Pokemon.
Caught legitimately by Jessie or James, possibly Wobbufffet. He's outlived all the others and seems set up as their strongest and most versatile, he can tank most of the twerps when commanded properly. He's also been put to a lot more use in Kalos. I have a soft spot for Inkay and Gourgeist as well though. Kalos was a good region for the trio.
Jessie's Lickitung was pretty tough, in one episode it broke Brock's vulpix and Ash's Pikachu and Bulbasaur quickly, taking almost no damage. Then again I don't remember it doing much after that so maybe Yanmega or gourgeist was stronger. In terms of raw power though, James' Gyarados was probably the strongest (although he kinda released it before it evolved so maybe it shouldn't count).
I'll give noteworthy credit to Inkay, he's maybe the one Pokemon of the squad outside Meowth (and maybe Wobbuffet) that has been shown to be proactively loyal to Team Rocket. Nearly all the Pokemon Jessie and James obtain are faithful and even affectionate, but recessive and inactive outside following orders (Ekans and Koffing pointed it out themselves, they don't give a monkey's about Team Rocket unless Jessie and James order them to).
Inkay went the extra mile, someone screws over Team Rocket (especially James) he damn well wants retribution and goes out of his way to get it even without the others telling him to. He even gathered his own freaking army. And guess what, HE WON. For a cute little baby squid, this guy is pretty passionate and smart. I'd love to see this side of him reappear.