Usual reason, to see in dark or light depending upon which eye he uses, but he doesn't have time to remove it.
I thought pirates wore patches to make it easier to go from outside to in their cabins? So that it wouldn't be so hard to read in the dark or.. something. lol
Doesn't have to go pillaging to wear an eye patch, just so he's ready to go below decks because it's dark down there. You don't want to knock the rum over and start a riot. There aren't any first hand accounts of eye patch wearing anyway, so maybe he just likes the way it looks.
As others have said, they both seem evenly matched enough that it would be plausible for either of them to win. But, I'm a lot less interested in the realism, and a lot more interested in the purpose of these characters. How does it come about that you know someone has to die, but the decision of who is so meaningless that it comes down to petty quibbles about realism, as opposed to the impact on actual story?
I'm can't help but think of movie fights. As any Stunt Coordinator/Fight Arranger would tell us: every good fight scene is a mini-story. With its own Inciting Incident (first sword swing or punch thrown) Rising Action (the blows exchanged, swings ducked, one gains lead, loses it ... the whole dance...) Climax (moment of maximum tension) and Resolution (one wins... or one gets away... fight's over). It'll have a context. What scene leads into it? and What's the scene right after? What does the rest of the story need of those characters after? (Hint: the one the story needs is the one who won the fight, yes?) I can't place odds, because the fight doesn't stand alone: it's a scene inside a larger narrative that I don't know because I'm not writing it. My suggestion is set an end point, and yes, I'm saying decide the winner first. Write toward an end you already have already decided. The reader might not know how it ends, but the writer needs to. But remember, if you let it slip you know, isn't that called 'foreshadowing'?
Well, in the previous scene an alien and my human protagonist are sitting in a dilapidated castle. The alien is explaining that the human perception of reality is flawed, and it is why they have been unable to harness zero point energy or unify gravity and electro-magnetism. This is why human beam crafts are limited to 20% of the speed of light. But the aliens have mastered gravitational shielding and are thus able to travel at speeds approaching 90% of the speed of light. A close friend of the protagonist is on one of these alien ships (for a reason central to the plot), and he must break it to her that because of the time dilation involved at these relative speeds she will be long dead before he ever returns. Then the ninja jumps out of a barrel and attacks the pirate. I have not plotted what happens to them both next.
If your protagonist is the one fighting, and he knows she will be dead before he returns, what's he fighting for? (That one thing would depress the heck out of me before a fight). Take 2 sheets (digital or paper)... Fight-A (Pirate prevails). Sketch-outline the fight. Just needs to be a list of significant beats in the fight, through to finale before the end of the page. (Ninja's relatives are weeping, maybe (... except the lost uncle, who didn't even know his nephew was doing this kinda thing...) Ninja-flags fly at half mast...) Fight-B (Ninja Prevails). As above, sketch-outline the fight, carried through to the Ninja winning. (Pirate's relatives are weeping, maybe (except a lone uncle, "That's-a My Boy!") Ninja-flags fly over parades. There are marching bands, Can-Can dancers, fireworks ...) Having a third sheet, for the story after the fight, would really help, I think.
If there's a lot of room to move around, then the ninja will definitely win. As it is a science fiction story you're writing I'm going to assume that the pirate has a better gun than a simple flintlock pistol. In that case then the pirate may gain the upper hand if he managed to corner the ninja and simply shoot him/her in the face. You mentioned that the fight takes place on a ship. If this ship belongs to the pirate then he can use the familiar surroundings to his advantage. The ninja will be in unfamiliar territory. If those two factors are out of the question, then the ninja will win.
Never mind all that, who needs to win so your plot moves forward? No deus ex machina for the winner, mind you, just make it feasible as you can for whomever has to remain standing.
Well, I didn't want to mention this at this stage, but the pirate is in fact a cyborg and the ninja is a mischief of hyper-intelligent rats wearing a suit of human skin. The pirate can probably sustain significant damage and retain certain abilities. At least a couple of the rats should escape.