There is no known reason for why Peppermint Patty is called "sir." She is referred to as "sir" primarily by Marcie, although a lesser known character named Sophie is actually the first character to call her that.
A running gag in "Peanuts" is Marcie calling Peppermint Patty "sir," followed by Peppermint Patty getting annoyed and telling Marcie to stop calling her that. The two characters often appear together and are near opposites of one another. Marcie is book smart and encourages Peppermint Patty to do her school work. Peppermint Patty doesn't do well at school but is athletic, whereas Marcie is bad at sports.