If he is getting his powers from his belt and hammer then a EMP puts him down. If he is operating off his own 'godly' power then he is stronger than his earlier version (stated his power was stronger than the belt at some point) but I'm not sure if he is at the lvl where he can manhandle Tony like 616 Thor.
Then again he went head to head with Hyperion and did rather well so yeah I'll say Thor can win here. Screw it.
Only thing Ult Thor has is a more warriorlike personality, especially if he's going up against 616 Stark (which is to say, 616 Thor will see him as a friend).
I wish that all who argue for EMP's working on Iron Man would take a moment and come to the realization that if it were that easy, everyone would use it on him.