Well I think Naruto is faster than Sasuke only because if we look back at all of Naruto's power up, he not only gain power but speed as well. Kurama's chakra cloak, SM, KM, and BM; BSM didn't really show any speed feat but then again Naruto had no training in that form. Naruto was said to be on Minato's level in speed with just KM but he wasn't good at it when he first used it, after he trained some, he had a speed fight with A and was shown to be on Minato's level with A's, Bee's and Tsunade's responses.
Naruto used his speed in BM which Gai and Kakashi couldn't keep up with when he deflected the Tbbs and he used his speed again when he saved Kakashi from Obito when it was Madara and Obito vs Bee, Gai, Kakashi and Naruto. Naruto didn't have any training with BM either so naturally he wouldn't know how to fully use his speed like A or Minato can with their speed. Naruto's new base or "SM/pre-KM?" mode did show speed that was fast against Madara when they fought before Sasuke came.
Sasuke usually gain great control over his MS/EMS jutsus after using it for a short time in battle as he did with Amaterasu, Enton, and Susanoo. So if I have to judge them on who has the upper hand in speed currently then I would have to say Sasuke since he shown to be able to use his speed jutsu when he wants and seems to understand it well enough; also the why it works is still a mystery for others but Madara seems to start to understand it a bit while Naruto's speed have been inconsistent and only used here and there but haven't used it much when he should have.
