Trying not to spoil anything, but there is supposedly ship upgrades that you can get in Dunnage. Which vendor should I be looking for? I have been around the island a couple of times to no avail, no one seems to sell ship equipment.

You can buy all the ship upgrades from the "resupply" option on the town map. This works for every town.

Usually the town map will not be the first thing you see when you enter a town for the first time. Instead the first area of that town will load (the one with the harbor) and you can walk around. You can then simply click on the leave-area button again (right where you entered the area) and the town map will pop up. 

Ahh, so it's not at a vendor, but the re-supply screen. *facepalm*

Thanks!