In her 1983 book "How to Suppress Women's Writing" Joanna Russ outlined several methods of ignoring the works of women writers including Isolation, False Categorization and Bad Faith which creates a social system that ignores and devalues women writing.
In fantasy and science fiction writing, all of these tactics have been employed. Thus, most of the "50 Greatest Fantasy and Science Fiction Books" lists are almost exclusively men with three women writers thrown in to prove that the list makers aren't that sexist.
So here are SOME but certainly not all great science fiction and fantasy books written by (or featuring) female writers.