If the fight is an all out death match, the Naruto would win. Remember, Naruto has already surpassed Jiraya and Minato as a Sage and also perfected a jutsu that even the his father could not do(wind element rasen shiriken). Plus he has an almost unlimited reserves of chakura. However, if its just a friendly match to see who's stronger, then Minato. No father would ever let his brat kid beat him until he's matured.