Board Thread:Episode Discussions/@comment-1251315-20160929105457/@comment-1512913-20160930202558

Early in the manga, Naruto's chakra is said to be yellow and early drawings of his Rasengan are also yellow, but then later on it appears to be sometimes drawn blue, same as anime, on the covers etc. So I would say canonically Naruto's chakra is yellow, but blue is the signature/mainstream/popular color so it's used because of fans probably.