Stuff with which to attack a flying ship

[Radiating Gnome]

Aeolius, man, that's beautiful.

Harpies are good, low-level flying opponents. Many of the incorporeal undead can fly.

You've got the pegasus/hippogriff/griffon/giant eagle mounted NPCs, which can work very well.

Depending upon you campaign, that flying ship can be a very valuable asset, something that lots of local warlords/powerful figures would find very useful. Which means that there would be a lot of landlubbers trying to take possession. So lots of NPC threats are appropriate.

In my current campaign, the PCs had a flying ship for a short while -- and they may get it back again. THey used it as transportation to the site of an adventure, and tried to park it someplace out of the way. They left some guards on it, but those guards were not enough to hold off the warband of a local warlord that took profound interest in the ship. So they've lost it, and are stranded a long walk from home.

I love being a DM.

<shameless plug>
You can read a bit about the follies of my players in my story hour, the Heroes of Spittlemarch. </shameless plug>

 

[Hand of Evil]

Of course, one could always opt for a fiendish dire shark.

Back in the days of 1E there was a monster book out that had air sharks in it.

 

[Masked]

or...

Vrock.