I would prefer that you write a few sentences in which you're not sure which one to use.
Remember that "knew" is past.
unless you are saying that after the sex-change operationsI never knew that you were a girl!
Knew is in the past, so "are" is changed to "were". Why is it changed to "were"?
Good point about the sex- change thing. So...would you say, "I never knew that you are a girl?"