I am aware that instanceof is an operator and that is_a is a method.
Is the method slower in performance? What would you prefer to use?
I can't speak for performance -- I haven't measured anything yet -- but depending on what you are attempting, there are limitations with instanceof. Check out my question, just recently, about it:
PHP 'instanceof' failing with class constant
I've ended up using is_a instead. I like the structure of instanceof better (I think it reads nicer) and will continue to use it where I can.