Both teams worked on uncharted 1&2 it only after part 2 did they spilt into two. 

Technically they've both made 3 great games this gen. Seeing as they all worked on Uncharted 1 and 2 together.

I find UC2 to be a much better game than TLOU. Just feels more fun and the atmosphere isn't so gory and dark (something I'm getting tired of from video games).

I see your point, and yes they have said that there are people who have worked on both games. That makes perfect sense, but the key people who are behind the game, for example, game directors, lead designers and head producers are different for each game, essentially making 2 teams in one amazing studio.

That's not to say that they still don't act as one studio, they are still one studio, but they have split some of their workers in order to increase efficiency. That being said I don't think we'll ever see them label themselves as team A and team B, they are Naughty Dog, that's who they are.

Yup, this. There is no clear division between the two teams and therefore no team that is better than the other.

Uncharted 2 team, which I also presume is TLOU team.

Unlikely. The original team wasn't split. They obviously hired more people as making 2 games at once with the same workforce as you made 1 before is impossible.

Well the team behind the Last of Us was a lot of who worked on U2, and I'd have to say that team was better. But only by a little, because honestly all of Naughty Dog is amazing :)

i count them as the same entity just like i count all the same AC makers the same

I haven't played either of them and unfortunately won't get the chance to, but I think Unchartered 3 looks more fun.