As amazing as Ledger was, Nolan wrote the part and conceived of it in his film. It may not have been nominated for Best Picture, but its omission is why today we have up to 10 nominees instead of 5.
And I don't think it is in the same ballpark as The Godfather or Goodfellas.
But Hollywood producers, studio executives, and industry insiders do:
http://www.listchallenges.com/hollywoods-100-favorite-films-hollywood-reporter
As do an international group of professional film critics:
http://www.bbc.com/culture/story/20150720-the-100-greatest-american-films
I would also add on a personal note that I think Batman Begins is vastly superior to The Winter Soldier and I know that is not a rarity. I also think The Dark Knight Rises is a much smarter and better made film, but that I will concede is an unpopular opinion around these parts. But I suspect history will show one lasting far longer in popular culture, if only by association to The Dark Knight, it still will.