I think it's Hero of Kvatch, but then, Nerevarine has some good background story and
on the other hand, Dovahkiin's victory wasn't a part of a prophecy.
I like the concept of the Nerevarine the most.
"Greatest" in what sort of way? What criterion are we using to define the word "greatest?"
This is a good point. Without something to check against, this is basically asking "whose your favorite player character."
Big fan of the Dovahkiin and the Nerevarine, personally.
In that case, I guess I would have to say Dovahkiin. As I see it, the CoC only assisted in stopping the Oblivion Crisis. I don't think the CoC could have ended the crisis by herself.
That leaves the other two. In my opinion, the Morrowind crisis was less dire than the Skyrim crisis. I don't think it was Dagoth Ur's intention to use Akulakhan to kill everyone who lived in Tamriel. Whereas I believe Alduin would have. So, to me, preventing Alduin has done more good than stopping Dagoth Ur. So my vote goes to Dovahkiin.
My favorite player hero, though, is the Nerevarine. I like her because she is a bit more mysterious than the other two. I'm not even sure my character was the incarnation of Nerevar. I cherish that ambiguity. You rarely see it in video games.
Champion of Cyrodiil would be favorable for me,
but since this is for who stopped the greater threat, I voted Dragonborn.