Considering the issue has been brought up here, there is the Naughty dog answer:
http://www.neogaf.com/forum/showthread.php?t=1151608Neil was up late reading GAF last night despite his better judgement, so he wanted to address it. Essentially, when they cast the role of Nadine they didn't even have a look for the character yet.
They auditioned actors of all ethnicities, American, South African, white, black, etc. Laura Bailey won the part. Laura was Nadine when she auditioned, so she won the role. Then they started capturing scenes, while still working on art.
Then a concept artist drew a piece of art of Nadine as a black character, and Neil thought it was great, and Neil though it was a great opportunity to have a strong, prominent black character in the game.
But Laura was white, and they had internal discussions about that and it inviting controversy. So they decided not to finalize the look until they could actually see it in scenes. Meanwhile they kept capturing scenes with the actors they hired for the parts.
Months later, when they finally started to get character designs and animations and stuff into scenes they captured and could actually see everything in context, they thought Nadine was a great character and Laura's performance vanished into the part and you didn't see anything but Nadine and Nate as characters, so they decided not to change the character to a white character.
There's also a prominent white character that they aren't ready to reveal yet that's performed by a black actor.
IMO that doesn't save the fact that they have an habit of showing black characters mixed suspicion and aggressivity (Nadine downright kick the "lovable" main they spend building emotional attachment with)