skygiants

Seconding the mention of Touma from SPEC! Though, as Tari mentions, she deliberately chooses to throw all female (or uh... human...) socialization out of the window. Arguably she uses the fact that no one ever takes her seriously until it's too late, but I'd say the bulk of it is more that she... really doesn't give a shit about the consequences. >_>

Osawa Eriko from Boss/Boss 2 might also qualify. She isn't called a genius but she is undeniably brilliant and a lot of the first season has her dealing with male superiors who don't take her seriously on the basis of her gender (dealing in ways that do not involve punching them in the face). One of the subplots also has her mentoring a younger woman on the team who is a science whiz with terrible social skills! IT'S SO GREAT.

I know you're not a fan of crime procedurals but they seem to have the best examples I can think of XD;