All toilets
A Times Square Information Center (5.00/5)
http://www.timessquarenyc.org/about_us/info_center.html
Separate men's and women's room are on the right as you enter the building. If the door is locked, you can get the key from one of the desks inside the main hall of the visitor's center.
B Renaissance New York Times Square Hotel (4.67/5)
Walk-in from 7th Avenue, head IMMEDIATELY to the right, where the elevators are. Make eye contact with no one. Take the elevator up to the Lobby Level. Exit left, hug the wall, and there's your glorious restroom. Be mindful that The Renaissance just went through a major reno, and one of the features is dark lighting (oxymoron!) so it may be hard to find this toilet the first time. But trust me, it has saved me from embarrassment more than once, and it's worth keeping in your back pocket. Ahem.
C Marriott Marquis (5.00/5)
If you enter the hotel from the back (under the overhang between 45th and 46th) and go straight up the escalator, the bathrooms are around and on the right. Best bathrooms in Times Square.
D Crowne Plaza Times Square (4.00/5)
An one-floor escalator ride above Broadway brings you to an excellent Times Square sanctuary. Security guards watch as you go up the escalator, but don't let that intimidate you--there's a New York Sports Club on the 16th floor, so locals are always going in and out. Once you're there (SW corner of lobby floor), you'll find private stalls with full wooden doors, solitary space, and quality toilet paper. It's not perfect--ventilation could be better, and Crowne Plaza is certainly no Ritz Carlton; moreover, it's not exactly a well-kept secret. But it's certainly more than enough to satisfy this discerning toilet customer.
E Toys R Us (3.33/5)
Very clean, busy with lots of kids. Just go up the escalator and around the corner on the 2nd floor. Where I usually go when I'm stuck in Times Square.
F Utsav Festive India Restaurant? (3.00/5)
The restaurant is in the plaza area a few steps west from 6th avenue between 46th and 47th street. Reaching this bathroom will take cunning and confidence (and karma) but if you play it right you will be sitting pretty. The bathrooms are on the second floor (where the dining room is) to the right of the top of the staircase. Walk upstairs as if you're there to eat, and if you get questioned by the host you can just say you were down at the bar, which is on the bottom floor. This one gets an accessibility rating of 1 because of the risk factor involved.
G ESPN Zone (5.00/5)
Clean, private stalls with personal TV's for bathroom goers enjoyment. Located on first Floor not to far from street entrance, my personal favorite in the Times Sq. area.
H Dave & Buster's (4.67/5)
Just go 2 flights up into Dave and Buster's and follow the yellow brick road into the game room. The bathroom has two stalls. The handicap stall is HUGE. It's always very clean and quiet on weekdays. One of the best spots in the city.
I Rockefeller Center (3.00/5)
Downstairs in the concourse of Rockefeller Center there are several public restrooms for men and women.
J Chipotle (4.67/5)
This restaurant offers rather clean and easily accessible restrooms for both males and females.