It's a tough choice, but probably Sigma because he's literally a virus. After becoming infected by the Maverick Virus by defeating Zero prior to the first Mega Man X game, the virus mutated and became the Sigma Virus. He can corrupt Ultron and turn him into another body or into just another Maverick to do his bidding. Plus, the many bodies he has used throughout the series to fight X and Zero.
I would have to say Ultron. While I have no doubt Sigma has the intelligence and durability to give Ultron a good workout, Ultron just has too much of an experience advantage AND is used to fighting multiple super-powered heroes (including Thor AND the Hulk) simultaneously. Now, while Mega Man X (Sigma's main enemy) is a tough customer, he's NOT in the Avengers' collective league.