If we are just going by raw damage output, at lv 99 (on my save) they both have 18 PA. I'm comparing a ninja unarmed with max brave, vs a knight with two swords, total damage done.

NINJA
Ninja w/o martial arts: 648
Ninja w/ martial arts: 972
Ninja w/o martial arts, +4 PA (gear): 882
Ninja w/ martial arts, +4PA (gear): 1323
Ninja w/o martial arts, +7PA (gear+bracer): 1250
Ninja w/ martial arts, +7 PA: 1875

KNIGHT
Rune Blade/ Rune Blade: 504
Rune Blade/ Rune Blade, +3PA: 588
Excalibur / Ragnorok: 810
Excalibur / Ragnorok, +3 PA: 945
Excalibur / Chaos Blade: 1098
Chaos Blade / Chaos Blade, +3 PA: 1680

As you can see, only with knight swords do knights come even close, whereas ninjas are using gear available before the completion of chapter 3. And the top end for ninjas is much higher, and with a few accumulates will increase exponentially in combat.

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As for living longer, that is something that is debatable.
The knight will undoubtedly have more HP (~600 w/ store gear, ~700 w/ rare gear) than the ninja (~330). However, HP is not the only factor in living long. At the end of the game it is not uncommon for enemies to hit for over 600, so the extra HP can often end up being negligable and by dual weilding the knight gives up any advantage it had with a shield. Additional, deaths often come from status ailments in the end game.

All in all, avoiding damage entirely is the best strategy for survivability. The best method is typically killing enemies before they can act. It is well established that a knight with sufficient gear can instantly kill any threat, however a knights speed is considerably less than a ninja, meaning the kill rate will be sufficiently less, (unless an excalibur is equiped). Additionaly a knights move is considerably less, making target options considerably smaller. Even with move+3 equiped a Jump of only 3 will seriously limit mobility, and a bracer must be forgon in favor of boots.

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Take for instance:
Ninja w/o martial arts, +4 PA (gear): 882

You could equip this Ninja with Concentrate ( which is unatainable for a dual weild Knight), and Boots & Move +3, for a total of a Move of 8 and a Jump of 5. A ninja that could move anywhere on the map, hit through all evasion/block affects, and instantly kill (almost) anything is completely out of the ballpark of anything a Knight could be set up to accomplish. And with four accumulates, the damage would be enough to deal max damage even with a -25% zodiac penalty.



(I will agree ninjas non twinked out with unarmed attacks are overated.)