If you know where to look you can usually find a few strong female characters, but I don't think it's very even.
Series/movies/books/etc to look up:
Firefly (and Serenity) Anne McCaffrey's books Sara Conner Chronicles (or Terminator also) X Files Dr Who 5th Element Alien
There's also strong women in Star Wars, Star Trek, Babylon 5, Battlestar Galatica etc but are usually more support than main character I believe (don't know for all of them as I haven't seen all of them).
There's totally an imbalance. Sci-fi has the same problem as fantasy: it started off as the pass-time of white, upper-class British men, so now Sci-fi is predominantly white dudes in space, fighting monsters. Just like fantasy is white dudes in the woods, fighting monsters.
You get women in both, but with very few exceptions, they're a supporting role. The problem is that production companies think that it's not believable for a woman to want to do anything but talk about men. But I guess this is what happens when the heads of the companies are all men as well.
That's not the solution, would it harm the genre to change of its own volition? Most science fiction is so immature, it's unbearable. I am a lover of a good story and human beings make a good story.
I'd say yes, there is most definitely a gender imbalance in sci-fi, as most sci-fi writers are men. Now to be fair, many if not most modern sci-fi books have plenty of strong female characters. But the prominent ones are almost always gorgeous looking and "sexy," which gets annoying after a while.
HOWEVER, is it fair to tell male writers to stop writing male protagonists they relate to, and female sidekicks who are their fantasy babes? When female writers often if not usually do the same thing, just in gender-reverse? I'm not sure it is. I think people should write what they want to. The gender imbalance isn't a good thing, but it's not necessarily the fault of the people currently writing; it's caused by the people NOT writing. If women want more woman-friendly sci-fi, we should write more of it ourselves (and I plan to ).
All that being said, people of both sexes should try to write protagonists of the opposite sex who *aren't* just their wet fantasies. (I'm looking at you, Stephanie Meyer.)