I suppose that technically, the head of the Covenant could have been Cloane. Arvin may have been the one to convince McCullough to help him create a Cloane that could do his dirty work for him while he was running Omnifam.
But the most logical choice seems to be Elena. It would seem to risky for Sloane to create the Cloane because there was never any guarantee he could control him. Also, it seems Elena has been able to avoid Irina, the CIA and the KGB for like 30 years now, so it is very conceivable that she has been planning and plotting this whole time and creating an organization that would help her reach her goals.