Factual error: In the opening credits of season 3 and season 4, when all of them are on the swing, you can see a palm tree in the background. If the show takes place in Massachusetts, why would there be a palm tree? Palm trees don't grow in Massachusetts.
Factual error: When Joey and Pacey go down to the Basement to talk, they catch Dawson and Gretchen kissing on the basement couch. They are lying on the bottom cushion of a couch raised above the floor. But when Pacey is talking to Gretchen about it in the kitchen during dinner, he says something about "Catching her and Dawson making out on the Basement Floor". He definitely uses the word floor, but Dawson and Gretchen weren't down on the floor - they were up on the couch. (00:23:25 - 00:26:05)
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.