Is Master Chief a girl or a boy?

Master Chief is most definitely male. In the games, his voice is clearly male, and he is always referred to as male. In addition, the official backstory has him being a boy named "John" prior to him being selected to become a Spartan.

Master Chief is a rank not a name, in the halo trilogy the main character is a spartan by the name of John-117 who is a male, but there are female master chiefs.