An age old question, with an age-old answer.
It's an interesting story actually...Ninjas and Pirates used to be the best of friends and were for many, many years paired as roommates. Each Pirate had a Ninja roommate and each Ninja a Pirate roommate. It was a natural relationship that worked quite well for many years. They would take picnics on the ships and swim in the sea together. They would play pranks on each other where Pirates would loudly storm into a town only to discover the Ninja had already snuck in and killed everyone without a sound. They enjoyed diving competitions off the ship's diving board and the Ninja would flaunt their skills with various high dives and trapeze-like acrobatics off of the various masts of the ship. The Pirates would teach their Ninja roomies how to swear, swashbuckle and ravish women, and the Ninjas would teach the pirates how to keep their blacks from fading in the wash.
Household chores generally entailed washing of the scabbards and throwing stars, repairing things broken in the previous evening's revelries (between the swordfights and the stealth attacks, enough damage was done that they rarely got their security deposits back), and of course general dusting and cleaning of all dirt and blood marred surfaces.
Ninjas of course are a little more fastidious, tidy, and OCD than Pirates, and even though they both worked the night shift it was generally the Ninja who were up first to clean. This may seem like an unfair arrangement, but the Pirates provided other services to the Ninja that helped even the score. You see, for many years the Pirates had been providing both women and drink for their Ninja friends. Ninjas of course being notoriously ugly under their masks and only having occasional success with the whole "mystique" of a secret masked-man sneaking into a woman's room after midnight; Ninja had very little success in locating available and willing women and even when they did, their habit of killing them immediately after, made resources quite scarce. So Pirates brought and shared women for their Ninja brethren and since their Ninja friends refused to have any pockets for carrying an ID and moreover refused to have their pictures taken, the Pirates also purchased or otherwise obtained all the alcohol for their parties.
Then one day a young Ninja, fed up, and ignoring some of the "fringe benefits" of his pirate roommate, finally got tired of hauling about big chests of pirate booty. They were on their 17th move that year, their 17th security deposit, and each and every time his Pirate roommate and he got a new apartment his roommate would suddenly have a pressing raid, or a hat fitting, or a sword fighting lesson and would never be around to help out. The Ninja ditched his roommate’s stuff, and secretly moved into his own place. Soon after he began bragging to other Ninja about his Spartan, minimalistic, "no-heavy load" lifestyle and soon all the Ninja were eschewing material possessions and refusing to help carry chests, swords, barrels and whatnot with their Pirate friends and roommates.
So the jilted Pirates moved out of their apartments, gathered their belongings onto their ships and moved onto the sea altogether so that they wouldn't have to deal with what they thought of as the Ninja's attempts to get out of hard work and jealousy of their riches, women, and ability to purchase alcohol legally.
So, now that the Pirates were all living on their ships and the Ninjas weren't "getting any" they were all a little depressed. The Pirates began letting themselves go and had such bad hygiene that their teeth began to fall out, and their beards got ragged and they smelled so bad that occasionally the captain would have to force someone off the diving board just to get rid of the stench. Several times a depressed sailor, sad, and overladen with filth and personal belongings, would just give up on his life and sink to the bottom, hence the term "walking the plank" became less about the sport of acrobatic diving and more about a man's last stinky breath.
The ninjas were depressed too, and began to meet in the dark of night and have parties on the "down low" and since they were in their ninja gear, no one could accuse another of having seen them at these parties. They prided themselves on their clean, simple lifestyle and put up signs refusing admittance to "stinky pirates and the unclean" from any of the side businesses they secretly ran (mostly hair salons, dance clubs and sushi restaurants).
The pirates found out about the ninjas nighttime pursuits and told all the women in all the ports they visited about the sissy men who couldn't get women who might sneak-in in the dark of night. The women lost all their fear and curiosity of the no-longer-mysterious ninjas and would simply laugh at them whenever they snuck in.
This revelry has lasted generations, and most Ninja and Pirates no longer remember the great symbiotic relationship their two peoples once had, and only have been taught to mock and ridicule their counterpart, or occasionally to flip out and kill each other.
This enmity has endured to this day, and they still don't get along.