The fees for pistol licenses are set by statute. See the opinion of the NYAG that states one $3.00 amendment fee covers all transactions made at the same time.
caselaw.lp.findlaw.com/nycodes/c82/a72.htmlNew York State Consolidated Laws
Penal
ARTICLE 400
LICENSING AND OTHER PROVISIONS RELATING TO FIREARMS
§ 400.00 Licenses to carry, possess, repair and dispose of firearms.
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14. Fees. In the city of New York and the county of Nassau, the annual
license fee shall be twenty-five dollars for gunsmiths and fifty dollars
for dealers in firearms. In such city, the city council and in the
county of Nassau the Board of Supervisors shall fix the fee to be
charged for a license to carry or possess a pistol or revolver and
provide for the disposition of such fees. Elsewhere in the state, the
licensing officer shall collect and pay into the county treasury the
following fees: for each license to carry or possess a pistol or
revolver, not less than three dollars nor more than ten dollars as may
be determined by the legislative body of the county;
for each amendment
thereto, three dollars, and five dollars in the county of Suffolk; and
for each license issued to a gunsmith or dealer in firearms, ten
dollars. The fee for a duplicate license shall be five dollars. The fee
for processing a license transfer between counties shall be five
dollars. The fee for processing a license or renewal thereof for a
See the NYAG opinion:
www.oag.state.ny.us/lawyers/opinions/2005/informal/2005_7.pdf