I'm not from the area, but I would fill out both.  The ATF papers with the C&R states repeatedly that you are still responsible for following state and local laws.

Call and check with the NY State police.  Better to waste time with extra paperwork than be someone's bitch in prison.

Heh, it's a pistol right Wave? Can someone without a pistol permit (non-cop) do the same? Not do any paperwork on it in NY? Of course you have to report it, and to tell you the truth before you receive any pistols in NY with the C&R you better look a little deeper into it. There may be issues with regard to NY State. Any pistol no matter where and how cops acquire it must be reported on the "Acquisition/Deposition" form within 10 days in NY, elsewise it's a misdemeanor.

One of the first aqusitions I got when the C&R licenses arrived was a Ballester Molina from Century Arms...the women in the primit's section had a fit because it didn't go thru a NYS licensed for handguns dealer, and they know me on a first name baisis.  Better jump thru the hoops even if it is a pain in the ass. Sorry