I think that the traditional comic world is still incredibly male-run. Most of the women in comics that I really love either do standalone graphic novels/memoirs or webcomics.
If you're looking for more traditional comics where women are involved, Kelly Sue Deconnick has several great comics. Bitch Planet, her runs of Captain Marvel, and Pretty Deadly are all amazing. Lumberjanes was created by and I believe has always been written and drawn by women. Fiona Staples (from Saga) has been drawing some of the new Archie stuff. If you haven't read/aren't reading Saga, do it. Emma Rios is another artist who always turns out amazing work. Unbeatable Squirrel Girl is drawn by a woman.
As standalone graphic novels, comic collections, or women who create webcomics, I am a big fan of:
Tomboy by Liz Prince/Liz Prince just in general
My Dirty Dumb Eyes by Lisa Hanawalt
Everything Julia Wertz has ever done
Nimona by Noelle Stevenson
I Think I'm in Friend Love with You by Yumi Sakagawa
All of Marjane Satrapi's work
Rent Girl by Michelle Tea
Through the Woods by Emily Carroll
All of Sophie Campbell's work (she is trans and most of her work is under the first name Ross)
I have Jillian Tamaki, Maggie Thrash, and the series Lady Killer on my to read list.
Also, I hate Alan Moore because of how often he relies on rape and extreme brutality to women as a storytelling device.