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I really liked Zahrah the Windseeker by Nnedi Okorafor when I read it last year- it's an adventure story with a female protagonist that reminded me of some of the Studio Ghibli films, and Okorafor's worldbuilding is really cool- all of the technology, from computers to buildings, is plant-based. I would consider it science fantasy, but I see it's more strongly tagged fantasy.
So You Want To Be a Wizard and sequels are quite good, also on the border of science-fantasy though.
A Wrinkle in Time held up for me when I re-read it this year; I was a little bemused at the overtly Christian parts, and I know that many people think that Meg is a rather passive character, but I would argue against that, and there are a number of other wonderful female characters as well; there's actually an interesting bit of gender-fluidity among the cast, with many of the non-human characters explicitly choosing to identify as female by human standards- it would be an interesting one to discuss. There is some definite iffiness about Calvin's mother being "the wrong type of mother" though, and some racial iffiness around the third book; I haven't gotten so far as to re-read any of the sequels, but I always liked the first two best.
What else... I remember liking Alien Secrets, and Enchantress from the Stars when I read it (though I was past the target age by then), A Tale of Time City (I can't remember whether I read much of Jones' other sci-fi), Shade's Children, H.M. Hoover's juveniles like The Rains of Eridan... I've heard a lot of good recommendations about Andre Norton but have never really been able to get into any of her work myself.
I read all of William Sleator's work that I could get my hands on, all of John Peel's children's Outer Limits and Peter Lerangis' Watchers books, and a lot of Bruce Coville (especially Aliens ate my Homework and sequels), but don't remember much about the female characters for better or worse in any of them.
An unrecommendation for The Golden Compass, which I liked well enough to read the sequels when I was younger, and tried to re-read recently- that book has internalized misogyny like whoa. Lyra is awesome because she is an honorary boy, other women are stupid and useless (eg female scholars at the university, who smell like cabbage or something weird) or beautiful but evil. (Evidently Will, the other protagonist who appears in The Subtle Knife, completely takes over the story from Lyra and everything becomes all about his issues for the last two books too, while she suddenly becomes clueless and incapable. Glad my re-read didn't progress any further!)
The Los Angeles County Library seems to have a very good list of Sci Fi for kids of various ages here: http://www.colapublib.org/reading/children/sci-fi.html
FWIW, I loved Jules Verne's Captain Grant's Children, aka "In Search of the Castaways." More advenure, really, but still some geography and science involved.