I arrived here following a link from ozarque's journal. I find this a very interesting discussion and hope you do not mind if I comment. I myself read sci-fi occasionally, fantasy all the time. You are probably right that there are few examples of strong female friendships in sci-fi novels. But there are actually quite a lot of them in fantasy, and I hope you do not mind if I list a few. Going quickly through my most accessible shelves of fantasy fiction I find:
Nyx and her cousin Meguet in Patricia A. McKillip's The Sorceror and the Cygnet and The Cygnet and the Firebird (I wish she'd write more in that series)
Erin and Aeriel in Meredith Ann Pierce's The Pearl of the Soul of the World (third in her Darkangel trilogy)
Ariane and Sylvie in Greer Ilene Gilman's Moonwise
Aidris and Ortwen in Cherry Wilder's A Princess of the Chameln
Faris and Jane in Caroline Stevermer's A College of Magics
Julianne and Elisande in Chaz Brenchley's Outremer series (this trilogy by a male author puts the two girls and their relationship at the heart of the narrative)
Barbara Hambly's Sisters of the Raven and Circle of the Moon.
Peony and Rosie from Robin McKinley's Spindle's End have been mentioned above.
A sci-fi example: Lynne and Ruric in Mary Gentle's Golden Witchbreed and Ancient Light
I have made a point of skipping books in which the friendship has an erotic side. But I can't miss out Laurie J. Marks's Dancing Jack: two female friends in this book, Ash and Rys, are finding out if they can be lovers. But there is a third important female character, Macy, who is a friend to them both.
Female friends in fantasy
Nyx and her cousin Meguet in Patricia A. McKillip's The Sorceror and the Cygnet and The Cygnet and the Firebird (I wish she'd write more in that series)
Erin and Aeriel in Meredith Ann Pierce's The Pearl of the Soul of the World (third in her Darkangel trilogy)
Ariane and Sylvie in Greer Ilene Gilman's Moonwise
Aidris and Ortwen in Cherry Wilder's A Princess of the Chameln
Faris and Jane in Caroline Stevermer's A College of Magics
Julianne and Elisande in Chaz Brenchley's Outremer series (this trilogy by a male author puts the two girls and their relationship at the heart of the narrative)
Barbara Hambly's Sisters of the Raven and Circle of the Moon.
Peony and Rosie from Robin McKinley's Spindle's End have been mentioned above.
A sci-fi example: Lynne and Ruric in Mary Gentle's Golden Witchbreed and Ancient Light
I have made a point of skipping books in which the friendship has an erotic side. But I can't miss out Laurie J. Marks's Dancing Jack: two female friends in this book, Ash and Rys, are finding out if they can be lovers. But there is a third important female character, Macy, who is a friend to them both.