What did Captain Janeway specialize in at the academy? If no specialization is known, what is known about her education at the academy?
The only conclusions we can draw are that Janeway had a passion for science, and studied enough of it to be posted as a Science Officer. She maintained that interest as a Starfleet Captain.
I always got the impression that, while Janeway was a Starfleet officer through and through, she thought of herself as a scientist. Her Memory Alpha entry tells us that, yes, her father raised her to be a skeptic, and to look at the world as a scientist would. It also says that, before serving on Voyager, Janeway posted as science officer on more than one occasion.
Janeway had no particular specialty at the academy; what we know of her academy years tells us about her as a person but is not particularly illuminating in terms of her specialty.
But watching the show, one will notice many times that Captain Janeway can pick up on scientific concepts quite easily. And there are several times that she works on a thorny scientific or engineering issue on her own. In the episode The Omega Directive, Tuvok calls Janeway "a woman of science".
So while her background may not include a formal scientific or engineering specialty, she certainly has the aptitude for these fields.
According to Memory Alpha
"When she was a cadet in Starfleet Academy she had a close relationship with Boothby, who brought fresh roses to her quarters each morning. She also enjoyed spending her time at a little coffee shop on Market Street known as the Night Owl. (VOY: "In the Flesh") Her love of coffee and her late nights got her through many of her classes, as she often had to pull all-nighters. (VOY: "Good Shepherd") She studied under such memorable professors as Patterson, Hendricks, and H'ohk. (VOY: "Relativity", "Friendship One", "Darkling")"
As a Starfleet graduate she would have been familiar with Ethics, Starship Mechanics, Mathematics, Chemistry, Astronomy, Piloting, Alien Physiology and a host of other relevant subjects.
She mentions having nightmares about a "Fractal Calculus" final exam and having taken a special interest in "Klingon Physiology" due to a particularly memorably visiting Klingon professor.
As far as her "speciality" is concerned it's noteworthy that post-academy, she also studied Chromolinguistics [communication with light?], American Sign Language and the gestural idioms of the Leyron as well as Klingonese. (VOY: "Macrocosm", "Hope and Fear"). This gift for languages would obviously stand her in good stead for a first contact type role.