Do you have any light curtains? If yes, excellent. Mix two of them with rikku's overdrive. if not, mix up a couple of grenades, offhand you should probably have at least two of those, and they'd do decent damage.

Do you have any dragon scales? toss them. any other gems of that nature too. I'm assuming you're not too well levelled, so yeah.

Beat him down with a lot of overdrives, there's monsters in the ship so you can get them all build up. Use al bhed potions often, they're good for fixing poison breath.

I just kept him close up before I remembered that there were volleys of missiles, and beat him pretty easy. But like I said, I was pretty well levelled.
First time I played I had to reset five times before I got anywhere. but that was before I realized mixing light curtains was so awesome. (regen shell protect haste)