So you knight advocates are saying that all the years of training in the way of the sword a ninja goes through are going to be thwarted by a guy wearing armor whaling around a large sword and shield? You dont take in effect the actual agility a ninja has. Speed trained properly will overcome strength and defense. A true ninja will find a weakness and isolate that as his/her target.

On the other side of the coin a Knight is trained to handle his weapon to be more than "whaling" it about. He/she is also trained to defend its weaknesses.

Overall I think a Ninja will win, but the fight is a good one.

Now that I have that covered, I feel that that entire argument is completely off topic. this IS a Final Fantasy question and since none of this fall into play in any FF game, its irrelevant. In FF games Knights are superior because FF focuses more on strength and swords than speed and skill. Example: FF1. Knights were hands down the strongest class physically. Ninjas were decent, but Knights hit harder.
Another example is FFT. The only reason a Ninja may have the edge over a knight is the 2 swords ability. However take that ability and place it on a knight and you have a knight who is better. With one sword, knights beat ninjas as well. FF5 Knights are better than Ninjas too IMO. In no other game that I can think of (ff3 I havent played much, IDK if theres even a Ninja class) are there any Ninja/Knight comparisons. Sure Shadow is a ninja technically, as is Yuffie. However their system allows you to train them in any way you feel. So its down to you who turns out better. Yuffie or Cloud. Shadow or Edgar.

The ONLY "ninja" who has anything to say about greatness is Edge. But Kain and Cecil I feel equal him so theres a tie for that one. FF8, 9, 10, 10-2 do not have Ninjas.