I've lived in SF and Tokyo and spent time in NYC. @potatolicious is spot on with this post. NYC streets and subway cars are, generally, cleaner than the equivalent in SF. Crime's lower (per capita, not totals) in NYC than SF too. You also don't witness as much derelicts and gang bangers on an evening stroll down a NYC street as you do in SF.

@cletus was right about the job scene though. Most tech companies HQ are in SF and there's a wealth of jobs. NYC's tech scene is still up and coming. As we've seen with Austin , Seattle, and NC/Research Triangle, "up and coming" can last for a long, long time.