The first is incorrect, and the second is a strange mixture of the very formal and the less formal.
"For whom are you looking?" is so formal that it sounds unnatural.
"Who are you looking for?" is the most natural, though it's an unusual thing to say when answering a telephone call. "Who would you like to speak to?" is more natural.
(Ems beat me to it. I agree that How can I help you?" is what we usually say.)