Steven,

Last year I went through the process of getting permits to build a 1-1/4 acre pond in NY. I think a lawyer would be better than the friendly NRCS folks. I am sure you know the NY website https://www.dec.ny.gov/permits/6222.html. There are basically 3 hurdles. 1. Is it a designated wetland? 2. Is it a "protected water?" There is a map on the NY website that shows all the wetlands and protected waters. Both of these require special permits that are coordinated by your regional DEC office. You probably know that the Region 7 permit coordinator is Craig Ortleib (315) 785-2324Craig.Ortlieb@dot.ny.gov
3. The next thing they will ask is for your plans including dam height and construction, soil types, etc. If it is over 6' you will need a dam safety permit.
4. If you can pass all these hurdles, and you are planning on disturbing over 1 acre of soil during the construction process, then you will need to file a NOI (notice of intent) which includes a Storm Water Pollution Prevention Plan. https://www.dec.ny.gov/docs/water_pdf/constgp020001.pdf
To file this you will need the assistance of a qualified preparer (someone with COESC, CPSWQ after their name). This will be required for it to get past David Gasper at the DEC who oversees all such permits. It would be helpful if your excavation contractor had or knew someone qualified.
This is all doable but you need to get past 1 and 2 first. I found the regional DEC office friendly but focused on doing their jobs. A friend pointed me to a Stormwater Coalition in the next county that helped me prepare the NOI.

Good luck