I just did the LYS as DL pass rider and there was no departure tax. I only paid the usual $17 for US security fees.
I would check with your "child" employee at NW to get the correct answer
There was no tax on the JFK/LYS portion at all for employee travel--no cost at all.
Were you charged a zed fare plus misc taxes? Do you still have your ticket copy? It should have all the charges listed at the bottom left side.
Perhaps there is a difference of zed med or zed med high for dates of travel? \Maybe Jumper knows how to unravel the mystery?