Look at who they fought. It is an easy choice. RJJ. On another note, RJJ should have retired a long time ago.
Mayweather has no win even comparable to Jones' wins over Toney and Hopkins. As a matter of fact, i think those are two of the best wins of the last 20 years. I'm trying to think of some wins that are better than those two and can't think of too many.
Mayweather has never lost because he doesn't fight anybody. Roy Jones loses because he fights everybody. The same with Holyfield, Mosley, Toney, Hopkins, Trinidad or DLH, if you fight everybody eventually you meet your match and you lose. But if you win most of the time, even if you lose it does not effect your legacy. Holyfield's legacy is secure even if he compiles 10+ losses because of the champions hes beat and the amount of titles hes held. Mayweather is an ATG having beaten Mosley, DLH, Marquez, but he is not anywhere near Roy Jones Jr's level. He isn't even at James Toney's level, and this is because he wont fight anybody he is an underdog to. DLH was one fight and DLH was post prime when they fought. He avoids Pacquiao, Williams, Cotto, Martinez, Cintron, or anybody who people think can beat him and he fights all the fights everybody expects him to win. To be high on the ATG list you have to beat people nobody thought you could beat, many times. Roy beat James Toney when nobody thought he could win, he beat Bernard Hopkins when nobody know who either of them were, he beat Ruiz when nobody thought he could win. Mayweather beat who? Ricky Hatton? That is if you consider Hatton to be on the level of Hopkins, Pacquiao, Toney, etc. Then you can say Ricky Hatton is his best win.
Stylistically and skillwise about the same, but Floyd is the much smarter if not more careful fighter. Styles make fights, and Jones fought sometimes outside his ability. Floyd is smart enough not to fight Pac/Berto and thus he remains UNDEFEATED!