High armor is no issue to deal with, use melee weapons, called shots/hit locations, Mana spells, Hit'em in the attributes, mind control, brick all his gear/wear, turn him to goo, there a long list of other options, take look at critter powers, make him run away in terror. Passing out heavy weapons to npc is just giving your PCs big weapons or some extra-cash. Nothing more fun then grabbing a tank, and seeing how long it takes the team to knock him out.
Or if you just like guns, just keep shooting, stun still kills. Once the target is out cold, then it really doesn't matter what type of damage you're using.