Pillars of Eternity II: Deadfire

In Neketaka, Queen's Berth, the shipwright is in the top left corner of the map. All of the ships are available to buy right from the beginning, but are too expensive to buy them for the first while into the game. He has an easy quest (The Shipwright's Plight) for dealing with some pirates which will get you 10% off all of his prices.

These are the prices, original / discounted

Voyager - 20,000 / 18,000
Dhow - 35,000 / 31,500
Galleon - 100,000 / 90,000
Junk - 120,000 / 108,000

A common issue with this game is items disappearing from shops. This unfortunately happens with ships as well. If this happens before you buy all of the ships, instead of buying them from him directly, when you land in Queen's Berth, select your ship as if leaving the map, go to the supply option at the bottom, and all the ships will be there as well. This was how I was able to get the one that disappeared, and it even allowed me to re-buy ones I already had, so I believe it doesn't rely on his stock. I cant say that it'll work 100% of the time, but it is at least a second option to get around this problem.