Mr. Krabs' Pirate Ship was a pirate ship. It appeared in a flashback in the episode, "Grandpappy the Pirate." Mr. Krabs sold the ship and fired his crew.
Mr. Krabs' Pirate Ship is a large wooden boat with many windows near the bottom. It also has a large sail at the top with a picture of a skull and cross swords.
In "Grandpappy the Pirate," Mr. Krabs says that the Krusty Krab used to be a boat, and that it was always called the Krusty Krab, but in the "Krusty Krab Training Video," he says that the Krusty Krab used to be a retirement home called "The Rusty Krab." This is a plothole, though it is possible that the retirement home and the ship had similar names by coincidence, and that Mr. Krabs purchased The Rusty Krab with the money made from selling the ship.