I was in the one on the lower level.

Have to agree, there is nothing wrong with the restrooms at Grand Central, they are clean and there are a lot of stalls so you (usually) don't have to wait.

The bathrooms upstairs at Crate & Barrel (60th & Madison) are always nice and clean, and the ones at St. Regis on 5th are good to (use the side entrance on 55th St. and go down stairs). There are also some on the concourse level at Rock Center. I think the most elegant ones are at the Mandarin Oriental in the Time Warner building - step off the elvator and turn to your right.

The Crate and Barrel on B'way and Houston also has very nice restrooms. Pearl Paints on Canal St has a restroom if you;re in the chinatown area. In the village, the Forbes Gallery is opened most days from 11-4 and also has nice restrooms (free admission to gallery). Lincoln Center is also a great source of public restrooms in the area.

The Pottery Barn at B'way and Houston also has a nice bathroom

I have read that the police will gladly allow visitors to use any police station bathroom in NYC... I'm hoping we don't have to test this assertion :)