In New York you do need a fishing license and need to follow state defined limits, this is the case for a stocking permit pond.
If you have a farm fish pond license, entitling the holder to manage the pond for the production of fish including control of undesirable fish and aquatic vegetation, releasing, stocking, and propagation of fish. Holders of a fishing license or persons entitled to fish without a license may take fish from a Farm Fish Pond subject to General Angling Regulations open seasons, minimum size limits and daily creel limits. Laws pertaining to seasons, size limits and daily take also apply to owners of private fish ponds unless a farm fish pond license is obtained.
Bottom line if you just want to stock you need a Stocking Permit, then follow the normal fishing license rules. If you want to stock and manage then you need a farm fish pond license. There is a restriction on which species you can stock and also how you can catch fish.
I just went through this with the local NYDEC. Definitely contact your local office to find out the rules.
