Here are some facts:
1) It cost the "dealer" nothing but his time to conduct a NICS check.
2) In NY there is a significant anount of time needed to hand write two P-12's (which will need to be mailed to Albany) log in/out the firearm(s) from his bound book, read over the 4473, and phone it into the NICS center ~3 minutes IF there are no delays in processing, then file it away.
3) Purchases made outside of your state of residence are not subject to sales tax. NY does however "request" that you report and pay sales tax on internet purchases.
4) The dealer should be collecting sales tax on the transfer fee being charged. Chances are if he's collecting salaes tax on your out of state purchase, he's pocketing the money.
5) Charging for a NICS check is bullshit! NICS checks are a required portion of being a licensed dealer, the only justification would be a transfer sale at a gunshow (required by NY law).
6) Keeping the doors open and making a living require money. Scerwing people isn't any way to do it.