N.Y. Rapid Trans. Law § 15
The salaries of the members of the board of transportation and the salaries and expenses paid or incurred in the exercise of their powers and duties shall be chargeable to such city, and shall be audited and paid as follows: The board of estimate, on requisition duly made by the board of transportation, stating the purposes for which such moneys are required, shall appropriate such sums of money as the board of estimate may deem necessary for the payment of such salaries and expenses. The city shall not be liable for any indebtedness incurred by the board, or any member thereof, in excess of such appropriations. It shall be the duty of the comptroller, after such appropriation shall have been duly made, to audit and pay the salaries and expenses of the board, upon vouchers therefor to be furnished by the board, which payment shall be made in like manner as payments are made by the comptroller of claims against and demands upon such city. In case of municipal operation all salaries and expenses incurred in connection with such operation shall be included in the expense of operation.
N.Y. Rapid Trans. Law § 15