I'm leaning towards the Nerevarine, seeing as most of the other heroes, however powerful they might be, are still only mortals, the Nerevarine on the other hand is immune to disease and age, that's a big advantage right there, plus, the Nerevarine has killed several gods in the game, granted, the members of the Tribunal the player could have killed were weakened due to no having access to the source of their power for a long time, and Dagoth Ur could only be killed after you cut him off from his powersource, but defeating gods is still no small achievement, even if some divine intervention (And no, I don't mean the spell.) was involved. Plus the Nerevarine had to face the ordeal of getting corprus and the various unpleasant Sixth House monsters, as well as dreams from Dagoth Ur, I'd imagine that it would require a strong mind to not become insane if one faced things like that in real life. Now, I can't comment on the deeds of the person from Battlespire or Redguard since I haven't played either of those games, doing some traveling and killing a mortal mage, even if a powerful one, as the Eternal Champion did, seems unimpressive by comparison, and while the hero of Daggerfall may have needed a bit of intelligence to deal with the game's more political plot, it doesn't necessarily require much actual strength, and it's not like the Nerevarine hasn't managed to get some influence of his own, being the Hortator of three houses and beig named Nerevarine by the Ashlander tribes (Though seeing as this was done under the threat of Dagoth Ur and some of the people voting for you really didn't seem to take their decision very seriously and just figured that since there's no harm in doing it, they might as well, one does not know how willing they would be to support you after the threat was gone, and Oblivion seems to indicate that the Nerevarine left that all behind, though maybe this was for the best considering later events.), the Nerevarine may also have risen to the top of one or more factions of your choosing, although most Elder Scrolls protagonists could have done that so it's somewhat irrelavent. Now, the Champion of Cyrodiil did a few great things too, but ultimately, stopping Mehrunes Dagon was a task that Martin had to complete, the Champion of Cyrodiil may have allowed him to get there, but when facing the Daedric Prince he could ultimately just watch Martin do what he must. Now, he did gain some powers in Shivering Isles, but these don't seem to work in Tamriel, so unless all characters were in Shivering Isles, it wouldn't be relevant.
Of course, trying to compare the powers of different Elder Scrolls heroes is somewhat pointless anyway, since they all faced different challenges in different games, and being as they never have to appear in each other's games, there isn't much need for them to be compared, it's kind of like asking which is a more powerful animal, a tiger or a lion, both have separate habitats, and are adapted to survive in their own homes, I'm sure neither would do very well if transplanted into the other's habitat.
From what I've read on UESP, it seems at one point or another Bethesda might've been messing around with the idea of actually letting the player take out Dagon, and there's apparently a leftover of that or something where he'll liquify or some such after getting damaged enough of if you use the kill command.
Even if Bethesda had considered that, it never entered the final game, and therefore is irrelavent.