I personally think Naruto is going to be both a Senju descendant through Minato and the descendant of a second clan (Uzumaki) who also has the blood of the So6P's youngest son (or perhaps a daughter we have yet to have introduced, that would be a crazy twist and who knows what she could have inherited from her father, the ability to chain down bijuu maybe).
The Uzumaki being blood of the Sage is pure theory based on my feeling that eventually Naruto will become as powerful as the Sage himself and to me it would make sense if he had an additional tie to the Sage to explain his eventual mastery of both the body and the eyes (yes I think he will end up with the Rinnegan). We'll see this week hopefully, if Sasuke shows his new EMS and they are Rinnegan instead, if that theory pans out.
The reason I think Naruto is a Senju is because of the hints that we have gotten about Tsunade being Minato's mother (who the father is though is a mystery to me, could be Jiraiya but could also be Dan). The problem is that so many people seem to never use their last names, is Tsunade, Senju Tsunade, or something else (Namikaze)? Was Dan, Namikaze Dan? Was Jiraiya, Namikaze Jiraiya? My guess based on Naruto's affinity for Toads, and his natural ability as a Sage makes me think it was more than just teaching that has him so similar to Jiraiya. It could just be that out of his love for Tsunade Jiraiya took an interest in her family, training both Minato and Naruto, but I have a feeling there is more to it than that.
In any case I think there is going to be a lot more to Naruto's heritage than just a single blood connection to the Senju. Of course that is just my theory and Kishi has a magical way of coming up with the stuff I never would have.