Again, not a female, but I have been living in Tokyo for 10 years as an expat and have come to know many expat women. As with all things it depends on your situation--are you coming to teach English, as an expat relocation for a corporate, or just to find work?
In general, if you really enjoy the culture and attempt to learn the language then it could be a very rewarding experience. There is no other country in the world that I have been to that are as warm once you become part of their community. On the other hand, I have had some friends that have tried to stay exclusively in the expat community here and have had less good experiences.
Although I agree with Kotaro that for Japanese women culturally embedded sexism makes the workplace a trying place, my feeling is that foreign women often are treated better. There is definitely a growing portion of society that is increasingly westernized and making life easier for expats in Tokyo--part of the challenge will be finding a place that is comfortable for you as an individual.
I travel a lot for work but always think of Tokyo as home. The culture, transportation, outdoor life (snow, mountains, and ocean both within a bit more than 1 hour), food quality, safety and nightlife are just spectacular.
Hope that is helpful.