Does NY state hold that a ketuba is a marriage license?
No. The ketuvah is no more than any other private pre-nuptual agreement as far as its legal effect in New York State. The marriage license must be obtained from a person who is authorized to issue the license (a town or city clerk) between 1 and 60 days before the wedding ceremony. It must be obtained in person by both parties.
The document must be the official form issued by the state of New York and obtained from the appropriate office.
As far as the effect of the kesuvah @DoubleAA has pointed to Is the ketuba enforceable in American law? in which certain provisions of the kesuvah were upheld because they were purely secular (religiously neutral) parts of a pre-nuptual agreement.
The Marriage License
Where do you get a marriage license?
A couple who intends to be married in New York State must apply in person for a marriage license to any town or city clerk in the state. The application for a license must be signed by both applicants in the presence of the town or city clerk. A representative cannot apply for the license on behalf of the applicants. This applies even if the representative has been given a Power of Attorney. Notarized marriage license affidavits signed by the applicants cannot be substituted for their personal appearance.
Is there a waiting period?
Yes. Although the marriage license is issued immediately, the marriage ceremony may not take place within 24 hours from the exact time that the license was issued. When both applicants are 16 years of age or older, the 24-hour waiting period may be waived by an order of a justice of the Supreme Court or a judge of the County Court of the county in which either of the applicants resides. If either person is under 16 years of age, the order must be from the Family Court judge of the county in which the person under 16 years of age resides.
How long is the license valid?
A marriage license is valid for 60 calendar days, beginning the day after it is issued.