And most of them are for free. In fact, I rarely find paid public toilets in Tokyo. Inside public or private buildings like a department store or a museum, you can find the toilets by following the signs like the one below.
The symbol of the Ladies room is usually in red or pink and for the Men's room it is in blue. It is simple, and similiar to other countries.
Yes, you can also find public toilet at Train stations or Subway stations. As far as I know, toilets at Subway stations or JR stations are not dangerous for women*. The majority of these toilet rooms are quite clean and many people use them. *However, it is better not to use them at late night if you see only a few people at the station.
I don't think you will have any difficulty finding a toilet during your travel in Tokyo, BUT using a Japanese Style Toilet is a little different than most public toilet in North America. In some parts of Southern Europe they have similar toilets.
The majority of toilets in Tokyo are western in style, however, there are still many toilets, especially at train stations or casual local restaurants that use the squat type of toilets.
Introduction of how to use a J-Style Toilet
Using the Japanese Style toilet you must squat. Stand over the toilet stool facing the side with the hood. Them squat over it and conveniently place yourself close but not to the point of contact with the stool.
For beginners, this might be an awkward position, but as the body does not contact the stool it is sanitary...that is why toilets at public place like train stations are of the Japanese style.