I have to say Sinister on this one. He's veritably indestructible and the only known time he's been " destroyed " and remained deceased was in the Age of Apocalypse when Nate Grey ( X-Man ) killed him using extreme amounts of his telepathy and telekinesis, both of which Magneto is void of. Magneto could rip his body apart for days and still wouldn't be able to kill him. While Sinister could use his own scope of telepathy to subvert Magneto.
Sinister has a contingency plan for everything and every mutant. He likely knows Magneto better than Magneto knows himself. You don't think someone who's been stalking mutants across the globe for well over a century wouldn't have Magneto's weaknesses and strengths pegged? I think he would. First of all as great as Magneto's powers are -- they just could not destroy Essex. He's too durable and too resilient. The only known weaknesses for him known are extreme and unfettered levels of telepathy and telekinesis used in conjunction against him. ( Ie; X-Man, Cable, Phoenix, Onslaught..etc. ) Magneto is neither of those so there's absolutely no way he's able to kill Sinister unless they change the writing. Second, Nathan Essex has a contingency plan for every known mutant across the globe. He's has EVERY mutants DNA structure mapped and memorized to the point he could probably tell you who Magneto's daddy was. Third, Sinister would never face Magneto head on. He'd either send in the Marauders, The Nasty Boys and or his recently created team of SUPER mutants -- The Children. Whom have all the powers of the X-Men and more. Super strength, speed, agility, optic blasts, telepathy, healing factor x's 10 etc. And then even after that he'd use his OWN telepathy to manipulate Magneto in some fashion. If he was easily able to shut down X-Man's powers then imagine what he could do to Magneto. There is no way Magneto would win against Sinister. He's not durable enough, smart enough or resilient enough. Magneto was killed by Wolverine at the end of Eve of Destruction....I think Sinister could easily take him.