The main bathroom at Penn station is located next to Houlihan's near the Amtrak waiting area and is quickly accessible from both uptown and downtown ACE trains by taking the staircase that is between the exit to the subway and the LIRR tracks. So now that you know how to find it we must recommend that you don't. It's filthy and the clientele is sketchy at best. It's fine for a quick piss (if you're a guy) but anything more than that and you will be praying for constipation. As you can see from the photo I wasn't able to document the actual fixture. The occupant of the single functional stall was holed up for longer than I could comfortably linger.