Normally you ask "what is your favorite pet?
" (here a question about pets in general).
But sometimes, but not so often, "what are your favorite pets/animals
?" Now to single out one or a couple of them, from a group - say, if are in a pet shop, veterinary hospital, zoo, etc. A place where you have many animals.
Or even in a general way, as the one above, but it´s used (with the plural form) once in a blue moon (or almost)!
So, if you use with the plural form you won´t be sued on it.
But if you use the singular you will be with more company!