I remember reading that the quote is often attributed to Gagarin because of a presumably apocryphal story told by his backup, and the second man in space, Gherman Titov, in his autobiography.

Said apocryphal story was that Gagarin, upon landing and being carted back off to Moscow for a parade, was cornered by Nikita Khrushchev and asked "did you see God up there?" to which Gagarin replied "yes, I did." Khrushchev frowned for a moment, then told Gagarin not to tell anyone. Minutes later the head of the Russian Orthodox Church cornered Gagarin as well and similarly asked him whether he had seen God up there, to which Gagarin replied "no I did not, Father. Don't tell anyone."

However, I am now having difficulty backing up that assertion, as Titov's autobiography is not well documented in English, and my searching is a tad lazy. But if memory serves, that is the origin of the quote (and Titov was known to be much more atheist than Gagarin).