==Duel==
Japan; 1600s
A local gambling attracted A hairy man goes to the bartender and bribes him with a heavy coin purse. "I'm lookin' for the wereabouts of 'The golden armor of Kagura Uchia'." The bartender gives him a scroll, with a map written on it. "A three days journey, if the sea winds allow it.' He then shoots the bartender dead and takes his gold back. The people were shocked of course, as he turned his guns to them. The bearded man was a Pirate, and he turned over his hat; asking the other patrons to 'donate' their money to them. But as he left, one of the patrons he stole from rushed into the forrests. This man was secretly a well known criminal too, a Ninja. He wore his dark clothes, carried his gear and went through the trails. The pirate was still headed for his ship, but before he left the tree line he hears the bending of branches and the rustle of leaves. Thinking someone was following him, he lit a grenado and threw it at the path behind him. In the flash of the explosion the forrest lit up, just for a second. Just long enough for the Pirate to see a black figure leap at him from the tree tops. He rolled out of the way of the Ninja, just in time, as the Ninja stabbed into the ground. By the time the Ninjato was pulled out, the Pirate sheathed his Saber in his right hand with a pistol in his left. "Is this 'black cat' in my path?"
The two slashed and stabbed at each other, but neither could land a blow. The Ninja made a defensive stance, but this allowed the Pirate to aim his pistol and fire. The Ninja ducked just in time, and he heard the bullet fly past his ear. The Pirate reaches for another pistol from his vest. The Ninja saw this action and threw three shuriken; two of which hit in the chest and shoulder. But the Pirate has a history of getting stabbed, as seen by his many scars. He pulled out the shurikens and taunted; "You can't kill a gull with a toy!" The Pirate had his own knife; he unsheathed and threw it at the Ninja. It landed and lacerated his arm, but it was only a glancing blow. Yet the Ninja knew that with his cover blown, he lost his advantage. The Pirate drew two pistols and aimed both at the Ninja's head. The Ninja was crafty however; he threw a smoke bomb into the ground. The cloud quickly faded, but so did the asssassin. He sees the bushes shake as the Ninja flees. The Pirate keeps his guns at the ready as he exists the tree-line. At the sandy beach his rowboat rests on the shore. He keeps an eye out, knowing the beach has no cover to hide behind. But as he pushes the boat back into the water, he spies the Ninja's shadow, swiming just under the tide. The Ninja rises up with his sword, but the Pirate blocks just in time with his own blade. With their blades locked, the Pirate uses his free hand to pull a pistol and fire it at the Ninja point blank; but the gun misfires. Frustrated, the Pirate instead pistolwhips the Ninja. The Ninja's ninjato is knocked out, but he carries other weapons. The Pirate charges, but the Ninja breaks open a black-egg and throws it at the Pirate. The Pirate flinches in pain as the dust of glass scrapes his eye. The Ninja then pulls out a chain. It whips around the Pirate's legs, and with a sharp tug, the chain pulls the Pirate's legs upwards and the Pirate falls onto his back. The Ninja retrieves his sword and prepares to land the killing blow. But the Pirate grabs a heavy pile of sand and throws it at the Ninja. As the Ninja flinched; the Pirate pulls out his blunderbuss. The Ninja is too close to dodge the mighty thundering blast. The shot drills into the Ninja's leg; amputating it instantly. The Ninja drops his weapons and lands into the sand hard. The Ninja watches as the Pirate steals his Ninjato and throws it into the sea. The Pirate readies his rowboat, and before heading out to sea, shouts. "A parting gift for the beached whale!" He chucks a grenado at the Ninja, and it lands mere inches away. He whispers. "You drunken bastard ape..." And the bomb detonates.
The Pirate rows back to his ship, sake in hand. He takes a big gulp. "Ack, my drink has been poisoned!" He takes a sniff of the bottle. "Arg, it's just a tad stale. I'll mix it with some grog."
==Conclusion==
Both of these warriors had the skill and experience to hold their ground against each other's weapons. While the Ninja's arsenal was diverse, it consisted of very light and often improvised weapons; which is what many of the Pirate's weapons were like as well.
Both were strategic, deceptive and excelent at ambushing in their own right. So while the Ninja had gear specifically designed for stealth and speed this advantage alone wasn't enough to be a game changer; especially since Pirates were known for launching surprise attacks as well. If we made a scenario where the Ninja ambushed the Pirate, we need to make a scenario where the Pirate ambushes the Ninja as well to make things fair.
And even if you did make the argument that the Ninja poisoned all of their weapons, the Pirate can do the same as well.
The deciding factor of this matchup is the same reason why the Medieval Era was surpassed by the Reinassance Era; guns.
The Ninja was a master of ambush, and so didn't carry long ranged weapons in his arsenal. But even if he did carry say a massive Yumi bow, the Pirate had a superior rate of fire as he could carry multiple pre-loaded guns into battle and the Musket has an effective range similar to that of the Yumi.
And not to mention the majority of the Ninja's projectiles were very light weight and were only accurate at relatively close ranges. And even if they did land on their target they were rarely fatal; while black powder weapons can easily pierce through bone and kill. And not to mention the primary projectile of the Ninja were throwing knives; it's not like the Pirates didn't use their own knives as well.
While it is true that there are historical records of Ninjas using muskets; those muskets were matchlock Arquebuses and so technologically inferior to the flintlock muskets Pirates used. The Arquebus was also relatively heavy and loud; a type of weapon that conflicts with the Ninja's iconic stealth.
Basically the Ninja would need to charge into the Pirate's effective range, avoid his projectiles and engage at close range. However as fast as the Ninja is, he's still human and cannot dodge grenade explosions or shotguns. Even a Ninja has his limits.