“*My favorite food are apples” is not correct English.

There are at least four correct ways to express your thought. First of all, it is perfectly correct and natural to say “My favorite food is apples.” This is because the subject, “food”, is singular. “Apples” is the predicate nominative, and has no effect on the choice of verb. If that bothers you, I suppose you could say “my favorite food is the apple”. Other correct options are “Apples are my favorite food” and “The apple is my favorite food.”