The Importance of Not Being Too Earnest - S6-E3
Other mistake: In the scene where Pacey and his Boss are out to lunch, his boss states that he just bought a car, so they head to a dealership. When they are walking in, his boss goes to a car that's kept in the showroom and dusts it off with a cloth as though that's the one he bought, since it is unlikely that he'd clean off a car that wasn't his. A car that someone just bought would not be kept in a showroom; it would be on the lot and ready to go, especially if the paperwork was already completed, as the boss stated when he said it was already signed and paid for.
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.