N.Y. Comp. Codes R. & Regs. tit. 21, § 1806.21
(b) The commission may modify and approve as modified, or may disapprove, a project if it determines that the project is not in the best interest of the conservation, development, management, or control of the basin's water resources, or is in conflict with the comprehensive plan.
(c) Disapprovals—other governmental jurisdictions.