I'd personally pay Carpentry if you were specifically building wooden ships, and then your skill would also be useable to build carpentry for houses etc.
If you wanted to make a broad range of vessels I'd say it would be craft:ships.
As an aside, I'd also consider a few ranks in Profession:Sailor or Profession:Shipwright or the like, just to cover all bases.
First off Master Craftsman allows you to make magic items each item has a skill listed that you need so unless you are actually seeing items with Craft Ships (which would actually probably profession shipwright) then you can't make anything.
Second if you have actually found enough items to make it work by raw you have to have the chosen skill to make the item. If your GM is lenient he might allow it to work in this case so ask him.
Historically, building wooden ships was highly specialized work with a different knowledge set from carpentry; carpenter and shipwright were not the same occupation. Anyway, that's approaching your questions for a historical point of view.
I'd agree Wrex, my suggestion was more based on the narrow set of rules we are working with - and trying to keep in mind that the rules not only create an abstract of the skills, but further add confusion by adding a Profession system on top of a craft system.
Specific and General all at the same time... it really doesn't make a lot of sense :0
Do you want to build a ship all on your own?
I think when ships were build there were a lot of men required. Some Shipwrights, some carpenters, some rope makers some other professions and a whole lot of unskilled workers.
Like I said earlier for those to work with Master Craftsman they need to be wonderous Items. And then you would see exactly what skill they required.
And doing a quick search I can't find any ship related Items that you make using item creation Feats. Though their might be some in a book I don't have.
Then without GM fiat you need craft ship.
Specific and General all at the same time... it really doesn't make a lot of sense :0
Yeah, I know what you mean.
I would say Craft (Carpentry) because you are working with wood and Profession (shipwright) for nautical knowledge would both be required for building a ship. Master Craftsman is based on your Craft skill, so you would be able to craft any wondrous item that is wooden.
Just my thought but a carpenter could probably make a "good" small boat or maybe fix some damage and a great house
Where as a ship builder could make a great ship and could make a simple house
Yes the skills are different but they are not that different in terms of skills
A carpenter can make something wooden that will float, keep the rain off, etc. It takes a professional to know how to build a ship and where to site a house. It takes a great deal of knowledge to be able to build an ocean-going great ship or a mighty tower.
Craft (carpentry) can combine with Profession (shipwright) or Profession (builder) and sometimes Knowledge (architecture & engineering) to achieve tasks.