Smartest female character in comics.

[Adam Allen]

Kitty Pryde is a genius, at least as Claremont wrote her. Just not a magic-machine-inventing type genius as we tend to commonly think of, I guess.

Nadia Pym is another of the magical-inventor type geniuses.

[Michael Watkins]

June Covington
Deidre Wentworth aka Superia
Monica Rappaccini Scientist Supreme of A.I.M

[icctrombone]

There was Alyssa Moy, a classmate at college. She and her husband Ted Castle were behind the Nu Earth project. I think she's currently considered dead ....until someone revives her.

Last I read, she was dead but her consciousness was placed in a robot/Android.