I'm thinking copley place/prudential too, btw Barney's, NM, and Saks. Actually, there's more niche at Barney's (malle, lutens, etc) than at NM or Saks. Between the three, I think there's good coverage. then you can find the Chanel exclusives in the Arlington st Chanel store.
I haven't been in Bos for a couple of years. Just did a quick search and it appears that the harvard sq old style store, Colonial drugs, has moved to another place:
I hope they still carry Knize Ten, probably the best thing they had.