At the beginning of the duel M.O.D.O.K. is invincible - so fight with his minions for some time and wait for the malfunction of the enemy's shield. When it occurs, switch into Thor and throw your hammer at the villain, so you can hit him during conventional melee fight. After first hit, the criminal will jump to the water - so you must spend some time struggling with his troops.
Notice that the whole sequence described above must be repeated for three times - only then the talking head will be finally vanquished.