The Amtrak/NJ Transit mens room just inside the Eighth Ave & 33rd St entrance--one of the sketchiest public restrooms I've been in, although I've never been to Port Authority--now has a changing table.
Go in the right side.
The Port Authority men's rooms are significantly skeevier than Penn Station. I don't remember seeing a changing table, but that mostly because I held my breath and kept my eyes fixed in a straight line directly in front of me every time I had to use them. I've changed my kid at Penn... I don't think I'd bring her near the bathrooms at the Port.