The original tune is "Farewell and Adieu to You Spanish Ladies", which shows up as early as 1769 (in a journal of the Nellie). Melville references the song and others in his 1850 novel White-Jacket. Upon deeper inspection this poem is full of images of uncertainty, fear, and peril (unlike the typical rendition of Spanish Ladies). Traveling the coasts of England, the song's narrator is far from rounding the Cape of Good Hope, unless we take that too as a metaphor.
A Deadlight is a nautical term for a piece of heavy glass set into a deck or ship's side to allow light.
The Deadman (or Deadman's Point), is today known as Dodman Point on the south Cornwall coast, near Plymouth.
The Sargasso sea is the bulk of the Atlantic ocean just east of mainland North America.
The Doldrums is "a popular nautical term that refers to the belt around the Earth near the equator where sailing ships sometimes get stuck on windless waters." Now known for periods of boredom or depression.
The Flying Dutchman is the legendary ship of Dutch captain Van der Decken, condemned to cruise forever off the Cape of Good Hope (ill luck).
A flipper as in "tipping your flipper" (waving) must just mean "hand"
A goney or gooney is another name for the albatross, a sea bird. One of the few companions a lonely sailing crew has.