In New York State, ALL handguns must be registered to the owner's pistol permit (a NY State permit issued by county of residence). In order to register pistol on a New York pistol permit, the pistol must come from either a NYS 01 dealer or be previously registered in the state and transferred between permit holders. You must be an 01 dealer in order to possess an unregistered handgun in NY and it must be recorded in your book. An 03 C&R FFL is meaningless in NY with respect to handguns.
Additionally, counties are legally permitted to enact restrictions on firearms dealers over and above those put forth by the Feds or the State. My friend in Nassau County, an 01 FFL holder, is restricted from dealing in handguns by the county government. He could have applied for a handgun endorsement, but they required him to make signficant (read costly) changes to his retail premise for added "security". He deals only in long guns.
As far as I know (except in NYC), with regard to long guns, an 03 C&R license conveys all the same priveleges to New York citizens as it does to the rest of the country... but ONLY with regard to long guns.