As far as I'm concerned with the SP, TLoU is the game of the generation.... probably. For me however, it's not a matter of an Uncharted titles competing, as I am not a huge fan of any of them. They aren't bad (...actually, I thought the first UC was pretty bad), but they simply don't compete with the best. Demon's Souls, Dark Souls, and TLoU are my top games of this generation (and btw, Dark Souls 2 is still on the way).
They each have their own problems, and reasons why after a certain point I won't be playing the MP. Thing is, this doesn't apply to Demon's Souls, as that is fun enough to always jump on, except that so few play it still. Next thing is, I'll probably be done with TLoU's MP this week or the next, as I am bored and sad every time I play. Dark Souls MP however, while I am still finished, I played for over a year. Third thing is, TLoU MP isn't necessarily done, and I will likely play again when new stuff is released, especially if there is a co-op introduced.
As far as the actual original question, I certainly believe that TLoU is ND's greatest game. I really enjoyed the J&D titles (first two anyway), but few games are capable of instilling awe as TLoU was.
I would still possibly pick Uncharted 2 over The Last of Us, but I'm on the fence about it. I really enjoyed Uncharted 3, even if a lot of you didn't. When I look back at both games, I would possibly put The Last of Us over Uncharted 2: Among Thieves. If you are referring to which one did I enjoy more on my first playthrough and overall first impression, then I might go with Uncharted 2. It's a close one.
For me The Last of Us is the greatest game from any developer that I have played.
I agree it's **bleep** near the perfect game. Hilarious name, by the way!