This has been a bad year for the major women in science fiction. I can't think of who is left aside from Le Guin and (somewhat) McCaffrey.
I completely forgot about Connie Willis! The world is now a little brighter. (Doomsday Book has a solid spot on my top 50 list)
I included McCaffery for her Ship who Sang and her Pegasus in Flight serieses. I agree that most of her stuff is fantasy with psuedo-science backing it up, but imho those two are focused enough on science to make the cut.