Plot hole: At the end of the episode, when Pacey and Joey finally sleep together, there is a moment before when they are both standing in front of the mirror talking. To the right of the mirror, there is a large window looking directly into the bedroom they are standing in. The curtains are pushed back, and you can see the outside through the window. Pacey and Joey make their way slowly towards the bed, making it clear they have one thing in mind. They don't seem to notice the window which would give full view to their bedroom and bed, and neither of them makes any attempt to close the curtains. Noone seems to care that anyone walking by would be able to look directly in on them while they are 'busy'. (00:39:25)
Plot hole: When Pacey and Joey run into Jen and Jack outside the restaurants, Jack suggests they all go to the pizza place near them. Joey and Pacey agree, and it is implied that all four of them are going to the same place to eat dinner together. But the next shot of inside the pizza restaurant only shows Joey and Pacey seated at a large table with Drue, Anna and the other guys. Jen and Jack are nowhere in sight. It isn't likely Jen and Jack wouldn't be seated with or near Pacey and Joey for dinner, since they suggested they all go there to eat.
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.