I'm a huge fan of both Aeryn and Ripley but I think I'd give the nod to Aeryn because we saw so much more of her and her character was allowed to develop over so long - just an unfortunate side-effect of tv over movies.
I am also a big fan of Kara Thrace, who hasn't been mentioned yet - I'm sure lots of people will turn up and say she wasn't heroic, that she was a bitch etc etc - but she was completely messed up, and she was heroic, and she was brilliant to watch - "the best shot in or out of the cockpit."
Aeryn wins though.