Depends what you want and music you play?
If your looking for a traditional all-round good humbucker the seymour duncan JB is a popular choice, or if you want more low end for metal tones you could get a seymour duncan Pearly Gates or even an EMG.
I found the single coil neck pickup to be quite satisfactory but if i had to choose an upgrade i would definitely fit a DiMarzio YJM.