Naruto has surpassed Kakashi - in terms of raw power. He also has an uncanny knack for setting the enemy up to be a sitting duck for his attacks.
But otherwise, no. In the Rasengan duel, Kakashi was using an attack that he would probably not have used in most situations. He was also allowing himself to go in a straight direction, so that they could see what happened when their Rasengans met.
We've seen Naruto and Sakura have a heck of a time trying to beat Kakashi in the second bell test, and they had to trick him into closing his eyes in order to steal the bells. (What would they have done if Jiraiya hadn't written that new book!) But 'til then, they weren't having much luck. Why?
Kakashi's intelligence, speed, experience, dodging ability (largely due to the Sharingan) and arsenal of attacks.
Naruto's new Fuuton Rasengan and RasenShuriken may seem to have the ability to negate the Sharingan, but Kakashi still has to be hit by it. That is something I don't think Naruto can still do.
But in terms of raw power, yeah, Naruto's on top now - not to mention he always had more chakra and stamina.