"How have you been?" - you haven't seen this person in a while, and this is a general inquiry about how their life is going. The person can answer with a quick "Just great, thanks" if the greeting was simply to be polite, or can give more details if it was a sincere inquirery.
"Where have you been?" - this suggests the person asking has not seen the person asked in some times and is asking what that person has been doing in the recent past. Although the question is "Where?" the response can still be "Been busy."
Student or Learner