Mediaeval plate armour is not completely impenetrable. Arrows, swords and pointed daggers will penetrate steel plate. A ninja could, in theory, stab an armoured knight through his armour. However, chain mail will stop virtually anything short of a battleaxe or war hammer. While it may not stop all blows, full armour will reduce or eliminate damage from most assaults. A knight's weapons, such as swords and halberds, have much greater reach than a ninja's non-projectile armaments. Of course, ninja are less heavily armoured and their weapons are lighter, so speed would be on their side in a duel. A ninja would have to dodge their way in close to a knight and do something particularly lethal; a knight, on the other hand, just needs to land one blow that's reasonably on-target and the ninja would be dead or incapacitated.

Another advantage is a knight's ability to parry. Swords and shields are effective for blocking attacks; a ninja's weapons are utterly useless in that regard.

Also, the entire 'purpose' of the knight just appeals to me more: valiantly charging into the midst of the most fierce fighting, as opposed to the ninja's way of sneaking about the place, looking for cheap and easy ways to pick off unsuspecting enemies.