I don't rate fighters only on their prime years. It's kind of silly. "Yeah, I was better than you, till I wasn't, and then I wasn't for a long time". Bernard Hopkins was better than Roy Jones for a looong time in their late career even if he wasn't as good in his prime. I'd take Hopkins overall career over Roy's easily. Hopkins was competitive at a high level while Roy was getting KO'd left and right. I'm sure Roy wishes he could have been as competitive. Give me Pac any day.
In Rummy's survey, I ranked them both in the 11-15 range with Roy just slightly ahead. In that ranking, I could take any group of five consecutive in the All Time group and shuffle them. So to answer the OP, they are about equal, with Roy maybe slightly ahead.
Manny is greater for longevity and career wise , but both fighters at their peak? No contest Roy was greater at his best than Manny was at his.
Pacquaio in his prime never looked invincible unlike RJJ. He did great things considering where he came from, but you cannot tell me that he's a better boxer than RJJ
If you're talking at their very best, at their peak, Hmmm I'd probably just side with RJJ, he was incredibly talented. I think the last part of his career with his KO loses has stained his legacy and reputation. But I urge any young fans on here who are not that familiar with RJJ at his best to go and have a look at him, he was simply amazing. Pacquaio also incredibly talented, I just think Roy moving from middleweight to heavyweight world champion was something very very special.
I look at how they respectively came back from their big KO losses (RJJ from Tarver, and Manny from KTFO6, JMM) Roy was NEVER the same after that Tarver loss, and subsequently was then stopped by the Road Warrior, then lost to Tarver again. Roy never went on to come back from being down in the same way that Pacman did. After being laid out by Marquez like he was would anyone have predicted that Pac would win another title @147 beating Thurman like 8 years later or whatever it was? Having also rebounded to beat solid names like Bradley, Mathysse and Broner? Whenever Roy stepped up his level of comp after his 'aura of invincibility' was lost, he struggled,and lost badly to names he would have schooled prior to moving up to Heavyweight. Danny Green KO1, Enzo Mac KO4??? One could even look at Pacs big KO loss to Marquez as a 'blip' to an extent, given how well he rebounded. Roy not so much. On the other hand, if Roy had retired after beating Ruiz, it might be a different story, but his resume and legacy has been tarnished a lot by not knowing when to quit. Was pleased to see Pacman retire, had visions of seeing him go down the same road as Jones
To me, there is a difference between greater and better. Roy Jones was better in the sense that he was the more dominant force. He had quicker hands relative to his size, was much harder to hit cleanly, was maybe the most athletic fighter we have ever seen, etc. Pacquiao, however, was greater because although he wasn't as gifted, he fought a significantly higher caliber of opponents overall, had superior longevity, and was THE Champion in multiple divisions, something Jones never achieved. In short: at their peaks I would rather be Jones, but after it was all said and done I would prefer Pacquiao's achievements.