NYC is a pretty safe place 99 percent of the time to be an atheist but I do leave that last percent for the crazies who if you encounter one whether your atheist or not at the right time watch out. But honestly this rarely happens in NYC though probably more or less often than you'd think. Just go with someone who knows their way around at first and you should be completely fine your more likely to be beat or robbed for being in the wrong neighborhood at the wrong time for your particular profile in way not related to your religious belief or lack thereof. If your going on your own just stay in tourist areas or around stay inside at night alternatively, ask your hotel or friends where its safe to go and if all else fails ask the police. People can tell an out of towner and if you walk around looking scared and vulnerable someone might see you as an easy target. If you find yourself in a neighborhood that makes you feel worried leave but don't make scene about it unless you actually feel threatened and then in which case the most feared people in New York are the crazies gangsters and cops and you can't pull off NY gangster or Cop so your best bet is crazy, act crazy (develop a twitch and say weird but non offensive things or some other form of crazy you think you can pull off) and people will most likely leave you alone cause they'll want nothing to do with you, (who knows what you might do).