Boat Handling and naval combat

[Irontruth]

If you make it an ability, make sure the ability encompasses most all aspects of ship-life IMO. I'd suggest specialties looking more like this:

Piloting - fairly obvious, steering whatever it is you're in.
Quartermaster - this is managing the ships stores, scheduling watches and crew assignments.
Building - building and maintenance on ships.
Deckhand - all the little odds and ends that don't fit in anything else, like handling cargo loading devices, tieing knots, rowing, using the anchor, etc. (especially useful if you do the advanced rule of substituting specialties with other skills).

Abilities are really broad based and having a skill only be used for piloting (essentially how you've got it laid out) seems far too narrow to me.

[Pytorb]

I was thinking that this would cover most aspects of ship-board life rather than just piloting, my apologies if it has come across that way.

Small Boats probably doesn't need any degree of specialisation and Large Boats covers being a member of a crew which would automatically cover both piloting (for the helmsmen) and deckhand as well as virtually any other job on board ship. Ship's Captain would cover piloting and most of the Quartermaster functions you've outlined as well as being in charge, whilst delegating the actual stores management to the Ship's Cook. Though upon reflection Ship's Captain should also cover the command functions of the Boatswain and a Pirate Quartermaster as well, whilst obviously fulfilling a different role, so perhaps a different name is needed...

Ship Building and major ship repair I would personally cover using the Trade Benefit and the Cunning Ability in much the same way as I would cover building carriages and wagons with Trade and Cunning rather than Animal Handling. Basic Ship Repair and Maintenance I would probably cover with Boat Handling (either small or large depending on the size) but not any of the big stuff. However I would assume that most good ship's carpenters (and ship's cooks) would have their respective Trades as Benefits.