There are certain Skills that are all but ever-present in a pirate-themed GURPS game.
Seamanship is the most common Skill aboard a pirate ship. Having points in Seamanship is what makes a person a useful crew-member. Since we’re talking about a 17th-century sailing ship, a point in Knot-Tying should be considered a prerequisite for Seamanship. A member of the crew who is going to go aloft in the rigging would be wise to invest in Climbing, as well.
The counterpart to Seamanship is Shiphandling. It’s the skill of directing the crew. Page 220 of the GURPS Basic Set: Characters tells us that one needs points in Leadership, Navigation (Sea), and Seamanship before buying Shiphandling. Only a handful of people will need this Skill, but it’ll be a key skill when it comes time to take a prize. Similarly, Freight Handling would be of great use to the crew, but only a few members would need points in it to supervise loading and unloading of cargo.
While Navigation (Sea) will tell you where to go, Weather Sense will tell you when it’s best to stay home.
A knowledge of smaller boats is likely to be useful and common. Boating (Unpowered) is required to take out a rowboat, while Boating (Sailboat) is necessary if under sail. Smaller boats can often transition back and forth from one specialization to the other, so it’s best to invest in both.
If a character is going to aim the cannon, that character needs to put points into Gunner (Cannon), while those using mortars will want Artillery (Cannon). Loaders and assistants don’t appear to need either Skill, though it could be helpful. A skilled crew might improve rate of fire, for instance.
Now that we’ve sailed up to a target and unloaded the cannon, it’s time for boarding. Most pirates are going to want some sort of combat skill for when the fighting moves from ship-to-ship to hand-to-hand. (Also useful for settling fine points of justice between sailors.)
The favorite ranged combat skill is Guns (Pistol), for flintlock pistols, with Guns (Musket) close behind, for longer arms. A TL4 sharpshooter might have Guns (Rifle), but they would be more commonly found on land. At TL4, it was expected that a gun would be fired and then be used as a melee weapon for the rest of the fight (see GURPS Low-Tech pg 63, under “Musket or Rifle” and “Pistol”), so a pirate might also want Axe/Mace or Two-Handed Axe/Mace for the follow-up.
The classic pirates’ weapon is the Cutlass, customarily used with the Shortsword skill. It also offers the option of a hilt punch, using Boxing, Brawling, or Karate. Other melee weapons commonly used during the Age of Sail include the boarding pike (not the Pike from GURPS Low-Tech, which has a Reach of “4,5”, but the Spear, with a maximum effective Reach of 2), the boarding axe (certainly used with Axe/Mace skill, but could use the weapon stats of a Hatchet, Axe, Small Axe, or even a Pick), and all manner of knives and improvised clubs.
Historically speaking, few 17th-century sailors knew how to swim. Cinematic pirates, on the other hand, all seem to be Trained By An Otter, and it works well for them.
Pirates who find themselves marooned on some deserted shore had better hope they have points in Survival (Island/Beach) or possibly Survival (Jungle). Knowledge of several languages is also quite common among pirates.
Regarding traits beyond Skills…
Sense of Duty (Brethren of the Coast) [-10] and/or Code of Honor (Pirate’s) [-5] are highly recommended. Remember, this isn’t an attempt to be true to history. The pirates might be unwashed, violent thieves, but they’re the Good Guys!
Most pirates aren’t rich (yet!), and the usual pirate load-out (cutlass, pistol or two, rags, bare feet) isn’t all that expensive. A Wealth level of Struggling or worse is recommended, but not required.
One who has been convicted of piracy, but not hung for it, might have Social Stigma (Criminal Record). They’re also likely to be sporting a stylish brand, just like Captain Jack Sparrow.
Speaking of which… being a pirate puts one firmly on the wrong side of somebody. In this case, that means Enemy (Spanish Navy, 9 or less) [-20] at a minimum, for nearly any conceivable PC. The price is based on “a city police department” from GURPS Basic Set: Characters, page 135, figuring that’s the default value for “wanted by the authorities”. A really famous pirate might bump up to a -30 point Enemy, if pursued by entire fleets or especially powerful ships. Off-hand, the only way I can see for a member of a pirate crew to avoid taking the Enemy would be if they could claim to be serving under duress. Such a state of grace wouldn’t last long. It’s hard to claim one’s innocence when caught red-handed, forcing captives to walk the plank.