How do I kill the Supreme Hunter in Prototype?
I'll assume you're on Normal difficulty.
Assuming normal difficulty:
Run around the deck whittling away at him with the whipfist. Whipfist can also be helpful to longshot grab a soldier to consume, but generally dash-grabbing does the trick. Keep your health high, and make sure to avoid his tentacle barrage. Your priority should be to remain at decently high health -- after that, see what you can do about doing a bit of damage. Let the military do most of the damage for you. If you're maxed out on health, give him a bit o' the ol' critical pain devastator.
In general, I kept moving and usually airborne. Stay at max whipfist range while airdashing/gliding to dodge when necessary. If you take a hit or two, feel free to speed your way to the opposite side of the carrier while you rest up and dine on marines. Don't bother with air attacks (whipfist excepted), as he will just block them.
When he hits (I believe) 30%, you'll get a counter and you'll have about three minutes to finish. A couple critical pains at this point should be enough to finish him -- this in mind, as he nears 30%, make sure your health is capped and don't use any devastators. You don't want to use one right before the timer starts and then not have enough juice to finish. There will still be a few stray soldiers to consume if you need, but not as plentiful as before. Wait for the timer to come up and unload on him.
If you didn't have enough to kill him, you have a few options: if he's very close to death, you may still be able to finish him off with the whipfist while maintaining safe distance. If there's anything left on the flight deck to throw, that can do a bit more damage. Last (riskier) option is to let him smack you around to give you an adrenaline surge, and give a last critical pain to finish him. I personally was able to finish him just on the critical pains from the health I had when the timer started.