In the manga, there was a note that crona's gender was undefined on purpose, and that they were just using "he" because they needed pronouns for Crona so why not? *Shrugs*
in episode 45, after Crona risked his/her life to save Maka, Stein and Medusa both refer to Crona as a "he". I have heard "he" mentioned multiple times, but never one "she".
MIKA is a boy.
Crona is a Crona.