What best conveys loneliness in this excerpt is the phrase "the correspondent thought that he was the one man afloat on all the oceans."
We are told in the text that the correspondent was responsible for a leak in what is probably the keel of the boat, enabling water to pour in ("a crest came with a roar and a swash into the boat"). However, he seems to be the only one really bothered by it, as the other characters don't let it trouble their sleep. The correspondent remains the only character awake on the boat and since they are in the middle of the ocean, it feels particularly lonely, as though he were alone at sea: "one man afloat on all the oceans".