The only time you would say this is if you had been told that you had a new teacher by the name of 'Miss Me.' A Chinese teacher, perhaps? Then, you might walk into the classroom and say 'Are you Miss Me?' In most other cases, your question should be 'Do you miss me?' (To which a possible answer might be: 'Only when I'm shooting badly')

Are you missing me? ( present continuous so it means Now or it is a temporary action)

Assuming there is no Miss Me to ask about... it'll be either Are you missing me? .. or... Do you miss me? And I'll assume this is about an emotion, not about the accuracy of someone's aim with a gun or bow and arrow. Are you missing me? Yes, but I'm getting better so I'll hit you any minute now.