As far as I can tell you are allowed to net your own minnows, provided you do not sell them, and that you use the minnows in the same body of water that you caught them from. (there are travel corridors listed also) Also you are limited to certain bodies of water to net minnows from. In other words, it is illegal to run out to your local TROUT containing stream and net some minnows. But it is legal at lake erie and the niagara river.

Here is the web page from DEC that talks about minnows, if you scroll down you will get to the part that talks about personally harvested baitfish.

http://www.dec.ny.gov/outdoor/47282.html

Now if anyone has any info to contradict what I just posted please add your comments.