I've been practicing a lot lately with large ships. I have used three bounty hunters and two bounty hunters with gunners and the doomshuttle. I have had great success with both lists and like that both give me 30 hit points and 9 attack dice a turn. Another option I had thought about was recon specialists and seismic charges over gunner. Which do you think would be preferable, two hunters and shuttle or three hunters?

It is all just a matter of taste and a question of what you face. It sounds like you may also want to try BHx2 with the Buzzsaw.

Going with Recon Specialist and Seismic Charge on a Firespray instead of the Gunner is certainly something to consider. A primary consideration to me there would be "how often is Gunner going to get used?"