Athena, Goddess of Widsom
Deadly Nightshade [Dr. Tilda Johnson]
Dr. Evelyn Necker
Dr. Kavita Rao
Lady Octopus [Carolyn Trainer]
Dr. Moira MacTaggert
Ruby Thursday [Dr. Thursday Rubinstein]
Starlight [Dr. Tania Belinsky]
Superia [Dr. Deidra Wentworth]
Thena the Eternal
the Witch [Dr. June Covington]
Ooh, this is a definite head-scratcher. I'd say it's probably between Alyssa Moy and Maya Hansen, based solely on their creations. As a side note, I think it would be great if Marvel actually had a woman in their frequently Amadeus Cho-referenced list of the smartest minds.
"When even one American - who has done nothing wrong - is forced by fear to shut his mind and close his mouth - then all Americans are in peril."- Harry S. Truman
OP, you listed Dr. Jean Grey, as a possible runner-up in the smarts department, but I do believe that she was only designated as a Doctor in the FOX Movie Universe. Please correct me if I'm wrong, but I do not believe she has accomplished this distinction in the Marvel 616 Universe.