I'm gonna go with Sarah Connor in this debate.
I think she is the most badass (even though this argument is titled "best", it quickly became "badass", so ok) because she has to live with the fact that judgement day is going to happen whether she wants to or not, and has to prevent her son from being killed by robots from the future. I don't want to incite another argument, but I think the terminators are much more deadly than aliens, especially the one in T3.
His argument that Sarah had to do a lot more to become this badass woman, is also really good. Ripely is around military guys so much that I think her ascent to badassery is not as impressive as Sarah's. Sarah literally goes from being a waitress to this super awesome amazon, saturating herself in as much combat experience as possible (for herself AND for her son, John).
My vote for best female protagonist in science fiction:
From a game: Samus Aran
From anime: Lina Inverse