The answer, according to Naughty Dog co-president Christophe Balestra, is that it fits neatly in between them. Speaking to French site Gameblog, Balestra says that Uncharted NGP is set between the first and second home console game, with plot points that run “parallel”.
He also adds that it will “most likely” interact with Uncharted 3 in some way, though didn’t go into details on that.
UPDATE: Or not! Balestra got in touch and told us “Actually I got this wrong 🙂 The Uncharted NGP story happens before the first one”. So it’s just a prequel, no sequel. OK?
Uncharted 3 et NGP : l’interview de Christophe Balestra [Gameblog, translation via Eurogamer]