I would say Nightmare Before Christmas, I've studied both pieces in Media Studies and we discussed the musical side of both of his films.
I think the reason Nightmare Before Christmas has better music score is because of its originality, when it was released it was so different to other films containing musical sequences at that time. They could delve into that darker side that not many other films had gone to before.
With Corpse Bride alot more of the elements Nightmare Before Christmas created have been used, making it harder to create a more original, outstanding music track. Even though the music in Corpse Bride is good, Nightmare Before Christmas has that little bit more edge to it, making it slightly better.