To be honest, a lot of characters are just female leads, why would they be the strongest? I would differentiate the female leads that were created by the player tho (especially in Bioware games), for the simple reason of the roleplay element. Mass Effect is one of my favorite games, I've played FemShep mostly during my numerous replays, but it's your choices, your personality that the character reflects. Okay, the character endures a lot and saves the galaxy, but I would still put them in a different category for interactivity. I would choose FemShep, your protagonist from DA:O and maybe the Boss from Saints Row IV.
My other favorites have been mentioned, and I'm glad: Jade from Beyond Good and Evil and Zoe from the Longest Journey. Both of them are amazing characters who do extraordinary feats. Best of all, most of the time while playing, I didn't even think about how the main characters of these games are women, it never even crossed my mind to make that difference, they were just people facing a huge challenge, people who made me associate with their stories.
Elizabeth and Ellie were rather strong characters too, but I wouldn't consider them leads. Elizabeth is a sidekick, Ellie is a deutargonist and an awesome focal character. I could see how people would want to put her on the list of the best, but unfortunately she's not a lead, so as sad as I am about it, she can't make my top leads list.