I just won against a whole load of ninja (about 6 or so, not sure) with support air from albowtross (plus some other units like healers and so on) playing chaos.
At first his group of ninja stealthed in and hit me hard, for a couple of runs - but then I knew his plan...
What I did was;
1. avoid using high tier units, so he has no high value target to kill, and so picked a juggerknight, my most threatening unit he coud reach.
2. a line of wings which he cant reach in front of the army - mainly so that to avoid them he has to stealth earlier than he'd choose and close. Also shots on any fleeing ninjas cant be a bad thing. If he brought in allbows, I backed up a little within in range of my dead, his albows vs my wings and dead was not good for him :)
3 a line of juggerknights to hack em after they break stealth and use stun to stop them escaping - with all that speed they can't run when stuned, and die in seconds when a jugger applies an axe to the ninja flimsy armour :)
4 a line of dead with poison to hit any ninja fleeing with poison and to counter his albows.
As he attacked I backed up my main army and sometimes he poped from stealth before stiking, and felt a hail of arrows and poisoned guts, then axes.
when he sucessfully attacked each ninja hit jugger and he took it to almost (but not quite :) ) zero health. (stealth 2, I think?)
but his ninja swarm became a pile of very resource-expensive dead as soon as they poped from stealth.
First wave I got some of them, second or third wave I finished them off and took him out before he rebuilt a significant fighting force.