It would be interesting to know exactly how "hogeye" barges got their name. The Oxford English Dictionary does not include the word and references are very rare. Whall(1910)is the earliest and best authority that the "San Francisco barge" meaning even existed. There's an American fiddle tune from before the Civil War called "Hogeye" or "The Hogeye Man," but without any melodic similarity to the shanty, as far as I can hear.

I can't prove it, but the original "hog-eye" man may well have been blind, or at least nearsighted enough to squint all the time. (Hogs have tiny eyes.) The Menasha (Wisconsin) Advocate of Jan. 18, 1855, p.2, refers to a "queer-looking, long-legged, short-bodied, white-hair, hog eye, funny sort of" feller. At least my guess is that his eye or eyes resembled those of a hog.

Wikipedia refers to eight tiny locations in the U.S.once known as "Hog-Eye," seven of them in the adjoining states of Missouri, Texas, and Arkansas. Some have changed their names. One chose "Haggai" as its "new" name. Perhaps they got their designation from being "a small compact place sunk in a hollow," as Wikipedia asserts.

It also asserts that the "Hog-Eye" in Vernon Co., Missouri, was "renamed Nevada in 1855." Maybe so, but the N.Y. Times referred to it as "Hog's Eye" on the front page of its issue of Oct. 17, 1861.
So "Hog-eye" and "hog's eye" were pretty much interchangeable.