A minigame in episode one of Strong Bad's Cool Game for Attractive People is aptly named Snake Boxer V. In one of the installments of Strong Bad's Cool Game for Attractive People, the Bear holding a Shark is shown as a Western Lowland Grizzlysharkasaurusbot... and it's holding a shark!
Ahem. Strong Bad's Decemberween wish list includes a catapult that launches balls of cobras and a chainsaw car.
And his fear of being fired upon with poison-tipped witch doctors.
"And then the pirate's like "No way!" and pulls out his musket. Actually it was more like a laser. Well, a laser sword. With guns on it. And it shot other swords."
"The ninjas all started flying, and some of them were turning into fireballs, and dinosaurs, and Presidents - wait, not Presidents, I meant volcanoes. The pirates were all flying on their burning sharks, and many of them were shooting angry bears. That were on fire. Cold fire."
Anicopters: Armageddon not only parodies mass-marketing kids shows via having a squadron of animal heads with elemental powers and helicopter rotors, but the Ninja Pirate Zombie Robot trope, as the credits display various characters that didn't even appear in the short, such as Captain Deadsaws (zombie pirate with chainsaw hands), Aborted Potato-Hitlers, Cannon Santa, and even Lucifer. The fake soundtrack credits also include a song titled "GIANT POTATO-HITLER VS. 2,000 VELOCIRAPTORS".
Chris the Ninja Pirate from Weebl & Bob. He's not that cool, though, so he may be a parody of this phenomenon.
The pirate being the natural enemy of the ninja, it's possible he's just supposed to represent a Thing That Should Not Be.
Blake Belladonna from RWBY is a Ninjabookworm who's also a former terrorist and a Cat Girl.