N.Y. Comp. Codes R. & Regs. tit. 20, § 8-2.5
Tax Law, § 1087(e)
No credit or refund will be allowed or made, except as provided in section 8-2.6 of this Subpart or section 8-3.4 of this Part, after the expiration of the applicable period of limitation specified in this Part, unless a claim for credit or refund is filed by the taxpayer within the period of limitation. Any later credit will be void and any later refund erroneous. No period of limitations specified in any other law or regulation will apply to the recovery by a taxpayer of moneys paid in respect to taxes under article 9-A.