All chakra is from the Juubi. Kaguya ate the fruit and gained the Juubi's essence. Rikudou was born with Kaguya's powers which is from the Juubi. Rikudou had the Rin'negan and all his abilities throughout his life stemmed directly from the Juubi.
Conclusion: The Rin'negan came from the Juubi.
I don't know if you've read my thread, but I'll post it here in quoted form that explains what I believe his power will be, but I believe it to be permanent. Naruto needs to surpass Hashirama, and it's the only way to do so, as gaining Kurama solely is not enough to surpass Hashirama. Only by a combination of the Juubi's powers (Rin'negan and Juubi esque mode) can he surpass him. Hence the only way Obito was able to break through Hashirama's Mokujin was because of the Juubi's power. That is what's needed to surpass Hashirama.
