There's not much in it, but I'd go with Jones I think. Pacquiao is greater p4p for sure, but the supermiddleweight RJJ was a very, very special fighter.
jone is better prime for prime slightly but pac is a much greater fighter. jones depended more on his physical abilities than pac when they were both in their primes. pac has made used of his skills more as he moved-up in weight.
I don't agree that Jones relied much more on the physical side than Manny. It is wildly overstated how much both men rely on their physical gifts IMO. Both Roy and Manny had insane physical gifts, but both had very high-level skills in their primes too. Jones-Toney and Pacquiao-Cotto are both performances of stunning skills.
Greater prime for prime? What´s that? Either you are better prime for prime or greater. Jones was the better fighter, at his best one of the best ever - sadly quite unproven against the best and afraid to take risks and thus his career never lived up to his promise, big underachiever IMO. Pac is the greater one though, he did more with less.
Tough question. Roy was more talented, but Manny has bigger balls, and so fought better opposition. If Manny is rated above Roy, its because of what Roy was reluctant to do, what Manny wasn't, same goes for Mayweather.
jones resume is very underrated i think and what he did to ruiz was amazing i know ruiz isnt a great fighter but he was legitimate top 10 heavyweight at the time and rj destroyed him if he had retired after that fight i think people would argue g.o.a.t