Cybernetic Ninja
First thing, you can't hit the ninja with ordinary weapons. He is extremely agile and can even reflect your Famas and Socom bullets with his Chokuto sword. What you do is fight him - hand to hand. Immediately walk right up to him and hit him with a three hit combo (hit the circle button three times quickly). Do that a few times and he'll want to fight you hand to hand. Now is when he gets tough.
The Ninja will come straight for you running. Do not let him catch you! Run behind stacks of computers or anything that will put space between you and him. Never stop moving!
He's got an attack pattern. Once he gets close enough to you, he'll do three roundhouse kicks, then do a series of backflips to get away from you. Careful, cause he moves fast on his attacks. Sometimes it's good to just rush him and get a three-hit combo on him before he can do his attack. A good tactic is to keep one of those "islands" of computers between you and him, making it impossible for him to hit you with his roundhouse attacks. If you have a lot of chaff grenades, throw one and it will temporarily screw with his electronics, enabling you to get an undefended hit on him. Keep doing this and he'll change his tactics.
If you hurt him enough, he'll slow down his kamikaze pace and simply walk towards you. This part is much easier than the first phase of his fight. Simply run directly towards him and continue running past him for a few feet. You'll notice he disappears and reappears a few feet away and throws a punch. All you have to do is run past him so that he disappears and comes back and throws that punch, then run back to him and give him a beating. Repeat.