Welcome to one of the most common problems we cabbies have. I sympathize, I can't pee in a bottle either, probably has to do with the fact that I'm a woman. To answer your question, almost all starbucks have restrooms. Barnes and Noble bookstores have great clean bathrooms and the one on 66th street and broadway is open until midnight. The Hess on 45th and 10th is also decent. You can always park quickly in the circle on 68th and york in the hospital and run into the restroom of the emergency room, that's a good one if you work the night shift.  Good Luck.