It's difficult where to place him with the Primarchs in consideration. We know Magnus is number two, and Lorgar certainly looks to be the likely contender for the next most powerful of the Primarchs, though who knows what others like Sanguinius could be capable of, or Horus after the Gods fuel him with their power.
Whatever the case, I would say Malcador is probably the most powerful psyker to have existed outside of the Emperor himself and the Primarchs, at least from all evidence. Just look at what he did with Titan, or that he was able to effectively brush off that hit from Lorgar at the ruins of Monarchia. Not to mention being able to power the Golden Throne for a significant amount of time.
Whatever machinations and ploys he ran behind the scenes, the Imperium irrefutably lost one of it's greatest and most powerful assets when he died.