Nyah, Rocket all the way! Manga Giovanni is the coolest ever, if you disagree with me then you're wrong. xP But I have other reasons for liking the team too...
First off, they're honest about their motives (You don't hear THEM going all "OMG! We're doing this for the good of mankind/nature/the whole world!"). Secondly, their plots actually make sense (Which is more than can be said for drowning the whole world or evaporating all oceans. <<). Third, their pokémon selection is best, since basically anything goes, and fourth, they have the best working conditions (No unbearably hot volcano lairs or cramped-up submarine rides for the Rockets. :P) and, presumably, the best pay-off.
Magma's uniform is kind of cool, but so is Rocket's, and the perks seem a lot better, not to mention that my favourite character from the anime is working for them. Three cheers for James and team Rocket, I say! ^0^