N.Y. Comp. Codes R. & Regs. tit. 20 § 50.2
The fact that two or more of the taxable events described in article 12 of the Tax Law and in section 50.1 of this Part occur within the State of New York with respect to a single transaction does not mean that more than one tax is imposed; only one tax is payable with respect to any one transaction. Thus, if a sale, delivery of the certificates and record transfer to the name of the purchaser are all made within the State, only one tax is payable. However, if any one of these taxable events occurs within the State with reference to any transaction, it is subject to tax regardless of where the others occurred. Thus, a transfer of record ownership on the books of the corporation within the State is subject to tax, even though the sale and delivery of the certificates were made outside the State. The same is true of a sale or agreement to sell, or a delivery of certificates made within the State, although all other events relating to the same transaction occurred outside of the State. However, Federal Law preempts the imposition of the tax on a transfer of beneficial or record ownership on the books of a corporation within the State effected through the facilities of a registered clearing agency or registered transfer agent if such tax is imposed solely because the facilities of such registered clearing agency or registered transfer agent are physically located within the State (see 15 U.S.C.A. section 78bb).
N.Y. Comp. Codes R. & Regs. Tit. 20 § 50.2