Superseding returns can only be filed electronically at the federal level.  You'll find this note under Miscellaneous Forms > Amended Return (1040-X)/Superseded, just below the section title "Superseded Return":

NOTE: A superseded return is a return filed subsequently to the orginally-filed return and filed within the filing period. The program supports electronic filing of superseded Federal returns only. A 1040X must be transmitted with a superseded return.

If you'd like to file a superseding state return, you will need to do so on paper.  You may like to consider filing an amended NY return instead before the deadline to make the correction should you like to avoid the paper route.

The Supreme Court had ruled in Haggar Co. v. Helvering, 308 U.S. 389 (1940), as was acquiesced in GCM 36932, that a timely filed amended return is to be treated as the original return or as a part of the original return.