I agree with the sentiment that it's near impossible to compare athletes, both in how they were great and their respective impact on their particular sport. Also it's hard to define 'greatness' , is it based more on pure skill and ability or their impact on the sport? And if both, does one have more weight or is it 50/50?
A good example of this, just in one sport., is hockey. A lot of people cite Gretzky (aka The Great One, TGO) and based purely on skill, it's a reasonable assertion. But what of Rocket Richard, Valeri Kharlamov, Gordie Howe and Bobby Orr? All were equally skilled and as dominant during their times, and players like Orr and Bobby Hull revolutionized the game with their innovations to the game (Orr being the first offensive defenseman, Hull first to use a curved blade). Gretzky's greatest impact on hockey was bringing the game to the West Coast. Hard to say whose the greatest when you factor in things like that. This is even harder when taking about the greatest American football player too.
Same thing with this situation. Jordan changed Basketball. Ali changed Boxing. But skill wise, I'd argue Wilt Chamberlain and Sugar Ray Robinson were more skilled and more dominant, of course marginally, but I think it's justifiable considering their records. So to bring this full circle, it's impossible to compare Messi to someone like Ali, or hell even Jesse Owens, because he's not political and a key asset of why these players are considered the greatest was their political impact.
Based on raw skill, Messi is better than Jordan, on par with Gretsky and Orr, and more successful that someone like Barry Sanders (IMO the greatest football player of all time) or Babe Ruth. The best athlete I can compare him to as far as dominance and pure natural skill is Bo Jackson. He's that kind of phenomenon where he simply does unthinkable things that no one else does and just dominates any game he plays in.
Lol despite this, I'll still say he is tied for Pele as the GOAT in football. I know, go ahead and castrate me.