That Was Then (aka Before and After) - S6-E16
Revealing mistake: In the very beginning of the episode, Pacey is watching TV and gets up to look out the window towards Hell's Kitchen. As he moves back from the window, he accidently bumps the kitchen counter/cabinets. An entire section of 'counter/cabinet' moves noticeably; revealing it to be a cheap, flimsily-built fake kitchen counter/cabinet instead of a more substantial, real one. This was obviously just part of a set.
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.