A historical source has been found for one variant of this quote. The source is Boris Bazhanov's Memoirs of Stalin's Former Secretary, published in 1992 and only available, so far as I know, in Russian. The pertinent passage, which appears near the end of chapter five, reads as follows (loosely translated):

"You know, comrades," says Stalin, "that I think in regard to this: I consider it completely unimportant who in the party will vote, or how; but what is extraordinarily important is this — who will count the votes, and how."