First off, I gotta say that Barak Mhornar has the worst unique footnote. I see no reason why you'd ever want to charge in the hero phase. Charge and fight, sure, but just charging is pretty lame lol.
Although, running and shooting turn 1 is really nice. I'd recommend the extra footnote 'There's no trading with some people', so you can get a few more extra mortal wounds on a character or unit to finish it off!
About the boats, they are not worth their points if you think of them for their firepower alone. You pay for their transport capacity, and the ability to limit your armies drops, which is really powerful.
Also, do you have any units not listed here?
I kind of wish your skywardens were also Endrinriggers, as skywardens are so overshadowed by how much better Endrinriggers are lol. But, they are a cheaper platform for the special weapons.
Your army is illegal, as you don't have three battline units, so you'd need a third unit of Arkanaught Company to make the army legal for 2000pts.
The last word is phenominal, I'd probably put it on the boat with the best gun. An Ironclad with the super volley gun and last word is really nice lol.
I'd also consider not taking the Endless Repeater, and giving the Aeither-Kemist the Athershock Earbuster. If your opponents units are not immune to battleshock, you can focus fire on a unit, blast them with the earbuster and then they'll loose extra models in the battleshock phase. Super deadly.
I'd also consider splitting the Thunderers into two units, just for ability to control objectives. It's more drops, buy you could always drop them all into one of the Skyvessels.
For making points for the third Arkanought Company, I'd probably drop the Edrinmaster or Navigator. Definitely the Endrinmaster first. I think you have too many points spent on characters, and I don't see the Endrinmaster or Navigator helping too much.