yes, they are from the kyubi, but as we have seen recently Naruto had them even before he was implanted with the kyubi. You could say that it's the result of being born from his mother who had the kyubi inside her at the time, and some kind of genetic abnormality was created, but In my opinion, Kishimoto just didn't think about the whiskers when he was drawing Naruto as a baby. He was simply telling a story of the main character and wanted the character to be recognisable to the readers. Without the whiskers, it simply doesn't look like naruto, readers would probably be like 'who is that?'. So I reckon it's an oversight by kishi, or something he just went with for storytelling purposes.