Women are underrepresented in a lot of roles throughout the world. It is usually due to some combination of social norms, expected gender roles, lack of opportunities, and old fashioned sexism.
It's also possible you simply don't see many female rappers because it's not the music you seek out. There are lots of very talented women in the rap scene. Though they certainly do not get the attention they deserve (see the paragraph above).
Edit: to answer the second part of your question, I'll go old school and say Rebirth of Slick by Diggable Planets. Missy Elliott and Lauren Hill are top-shelf, too. Other people here have mentioned Doechii; she's a new star on the rise.