A questioner is someone who asks questions, especially in an official or formal capacity. When a detective interviews a suspect, she acts as a questioner.
A questioner is also an interviewer, so if you're producing a radio piece, asking people on the street various questions, you are a questioner. An FBI agent trying to get to the bottom of a case is also a questioner, and so is someone who asks a question at a public event, like a lecture. You are also a questioner if you are having doubts about something, especially religious tenets — you're questioning them.