Little Goku, teen Goku, or adult Goku, they can all kick Naruto in the arse. Why? Dragonball/Z/GT is a martial arts series. Naruto is a ninja series. All Naruto does is disappear in a puff of smoke and jump from tree to tree...oh and he can close himself. Even without his saiyan powers little Goku was able to kick every one of his opponents ass because of his superb martial arts skills. Progress some years later and Goku gets new powers. He can shoot beams and make the earth quake. Naruto also gets new powers. He can also shoot beams but he can't make the earth quake, let alone destroy a planet with a finger. We forget Naruto isn't a strategist, he mostly relies on luck and openings he sees and takes advantage of. Goku is similar to Naruto in the fact that they both are hard headed (like really) but Goku actually uses his brain in fights.
Now, Goku vs Sasuke is another story...