I believe the origin of the phrase is from the Alan Clarke movie Scum in 1979 which depicts the Borstal system in britain. In the movie, Carlin is seeking his way to the top of the prison chain, to become what in the prison was known as the daddy of the prison. In one of the scenes, when the previous daddy has been eliminated, a triumphant Who's the daddy now!!! is yelled. The movie was apparently quite disturbing, but gained huge popularity because of the controversy it sparked, particularly regarding the borstal system.