100% Trakeena. Astronima was awesome by the end of In Space, but she started out pretty meh. Trakeena was a good character from the get go. First she was a daddy's girl, who didn't want to have anything to do with fighting the Power Rangers. She didn't want to become the ruler of her people, because it would mean becoming an ugly monster. She had to be taught how to defend herself. Then she was bent on revenge, when she was tricked into thinking the rangers killed her father. She eventually went insane, and became said monster, just so she could kill the red ranger. Even if it meant her own death.
I don't think there's ever been another ranger villain who went through so much character development throughout a season. I think she's also the only ranger villain to actually have a nervous breakdown, and go completely insane.
She's not just the best female villain, but one of the best villains, period.