Hello Ringoko,
As an answer to this question in that form in particular you could say:
"My favorite subjects are music and science."
"It is music and science" is not adequate ,you could use "it is" if you had one favorite subject to mention as in "It is music".
"They are music and science " would be a good answer to "What are your favorite subjects?" In that answer you would be replacing "favorite subjects "by the pronoun "they". However the question refers to one subject "what is.....". So you better mention in the answer "My favorite subjects" to show that you don't have one but 2 favorite subjects.
Another good answer would be:
" I don't have 1 favorite subject, I like both music and science" OR
" I have more than 1 favorite subject ,they are music and science." or simply
"I have more than 1 favorite subject; music and science"