I just completed this one-- This is how I take it, and I hope you can build something off of it:
As metaphors are similes without like or as, the entire poem is a metaphor in the sense that it's representing the end of the Civil War, but describing it as a ship and it's captain.
He shows the ship returning to port, how people are excited and cheering for the victory and the end of the war, but how the narrator is mourning the loss of his captain.
This easily represents Lincoln's death, which is an important aspect of the war and poem.