In the US, I was under the impression that we already had determined where the line is.
We allow our citizens to keep firearms in their homes. I have trouble believing that nunchaku or any other martial arts weapon is inherently more dangerous than a rifle or pistol would be.
Therefore it seems clear that the local law conflicts with federal law, and as such I would expect the local law to be overturned. The foregoing assumes that you can get a judge to hear the case, which it sounds like you have. Although I am curious... if the district attorney in New York has decided not to prosecute you, then do you still have a grievance to file in federal court? It seems like a judge might just decide to send you home until such time as you are formally charged. The city could just maintain the status quo by dropping charges against the folks who are willing to fight, and keep the law as a tool to control those who don't have the resources to mount a challenge.
By the way, if it isn't obvious, I am not a lawyer, so please forgive any errors arising out of my ignorance-- please do correct them, though, so I can learn more about our system.