Lee is naturally faster even without his gates mode, though Naruto's natural stamina will allow him to last against him for longer even without the use of SM.
Basically its:
speed + strength powerup
vs.
strength + durability powerup
in a pure taijutsu battle.
Lee's knowledge and expertise in taijutsu surpasses Naruto's skill with taijutsu, but Naruto's SM will allow him to survive some of Lee's Gate attacks. Naruto will have an extended attack range, but landing a hit on an opponent as fast as Lee will be very difficult.
It will depend how long Lee can last without his gates since using the gates will rapidly deplete his energy and will also weaken him by destroying his muscles if he uses it for too long. If he uses it at the right time, then he will be able to pull it off with difficulty. If not, then Naruto will likely finish him after Lee has been weakened enough by the strain of the gates usage.
