I think it ultimately comes down to what your view is on the progression of the sport. I personally believe the standard of football is increasing each and every year on the whole with the advances in sports science, fitness, money, more exposure and more competition.
I think if you put Ronaldo and Messi at their peaks on a pitch with the greats ( Pele, Maradonna, Van Basten, Cruyff, Best, Eusebio, Platini and even Ronaldo 9, Zidane, Del Piero, Figo - you get where im coming from), at their peaks, ronaldo and messi would look considerably better in terms of fitness and ability. However imagine Ronaldo de Lima was born a decade later and maradonna 27 years later - with the current advancements they very well may have been as good if not better than the present greats.
Comparing anything over a significant time period be it sports, cars, movies, architecture is very difficult because there's so many factors to take into account. The only solid data i guess you could use would be statistics.