After all of the speculation and questions on gun forums about storage of ammo in New York City, decided to look things up myself before considering reloading. Emailed FDNY from their site. Got a reply from Deputy Chief Inspector, who recommended I call their Explosives division at 718-999-1594, 718-999-1595 or 718-999-2710. At first, was told that FDNY doesn't allow/issue permits for storage in a private residence. After telling the inspector that it's for personal use, he said that FDNY doesn't care what you do in a private residence for personal, non-business, use. FDNY regulates businesses only. For personal, private, use, what you have in your private residence falls under NYPD, not FDNY. So, as long as you have a gun permit, you're all set.
Regardless, section 3306 of the NYC fire code, states that the 200 round regulation applies only to R-3 occupancies, which are kindergartens and assisted living homes and most definitely not regular private residencies.