Here's what Glostrad has to say:

A popular Christmas carol ever since the 17th century when a version appears in Forbes’s Cantus. The singability of the tune and the repetition make it an easy song to remember but the geographical and historical incongruities of the story make it a curiosity. The rumour has persisted that the song is actually about the skulls of the Three Wise Men being transported by sea to Cologne Cathedral in Germany. This theory seems reinforced by a copy sent to the Rev Baring-Gould in the late 19th century “as sung by the boatmen upon the Humber”, namely:

I saw three ships come sailing by,
I saw three ships come sailing by,
By, by, by,
I saw three ships come sailing by.

I asked them what they’d got on board.
They said that they had got three crawns (=”crowns” =”skulls”).
I asked them where they was taking them to.
They said they was going to Coln upon Rhine.

I asked them where they was bringing them from.
They said they was coming from Bethlehem.

But this is a single version from a single source and the trail runs cold at that point.

No mention of Hull.

Tradsinger