From a casual search, it appears to me that a Farm fish pond license is intended more for commercial use....what I would consider a hatchery pond. My take on the matter is that unless you intend to produce fish for sale, you may have the wrong license.
Granted, I know nothing about the rules and regs of New York, but I think a Fish stocking permit is what you really need, UNLESS you intend to produce fish commercially.
I think you're jumping through more hoops than may be necessary.
