Anyways, how Naruto does against Naraku is beside the point anyways...
Naruto is quite a bit faster than Sesshoumaru in Sage mode, and MUCH faster in Nine Tails mode, and you know how Sess toys with Inuyasha, only losing because of hubris. (And Sess also struggles with Naraku's shields, meaning just because Inuyasha has anti Naraku plot devices doesn't say anything about how he'd perform against other characters..)
He has the firepower, the speed, and most importantly, he has his clones. His MO is usually to send in clones, let them get destroyed, and use that information to form a strategy..
Assuming he doesn't just swamp him with over 100 Sage level clones from the start.