It's well-known in Newfoundland tradition, though I don't know where it originated. There are a few collections beyond Newfoundland. Also known as "The Gentle Boy." Lots of Newfoundland collections:

Gentle Boy, The (Why Don't Father's Ship Come In)

DESCRIPTION: "As I roved out one evening As I sat down to rest, I saw a boy scarce four years old Sleep on his mother's breast." They tell about his father who sailed away and was lost in a hurricane. "They cast their eyes to heaven and son and mother died."
AUTHOR: unknown
EARLIEST DATE: 1929 (Greenleaf/Mansfield-BalladsAndSeaSongsOfNewfoundland)
KEYWORDS: grief parting death sea disaster storm wreck baby mother father separation sailor
FOUND IN: Canada(Newf) US(MA,NE)
REFERENCES (6 citations):
Greenleaf/Mansfield-BalladsAndSeaSongsOfNewfoundland 113, "The Gentle Boy" (1 text)
Peacock, pp. 795-796, "The Ship That Never Came" (1 text, 1 tune)
Guigné-ForgottenSongsOfTheNewfoundlandOutports, pp. 330-331, "The Ship That Never Came (The Gentle Boy)" (1 text, 1 tune)
Lehr/Best-ComeAndIWillSingYou 120, "Why Don't Father's Ship Come In?" (1 text, 1 tune)
Lane/Gosbee-SongsOfShipsAndSailors, p. 37, "Why Don't My Father's Ship Come In?" (1 text, 1 tune)
Bethke-AdirondackVoices, p. 117, "The Gentle Boy" (1 text, 1 tune)
Roud #2973
RECORDINGS:
John James, "My Daddy's Ship" (on MUNFLA/Leach)
CROSS-REFERENCES:
cf. "The Rocks of Scilly" [Laws K8] (theme)
File: GrMa113