Nothing terribly cryptic going on here. The Great Wide Sea is about…the great wide sea. It literally takes place on the open water.
It's probably worth noting that the title does appear in the text itself, just after the boys are stranded on a deserted island.
We were on it. The three of us together. Lost in the middle of the great wide sea. (31.45)
It's not just any sea, either. It's the sea surrounding the Bahamas, an area that's almost totally devoid of people. The title emphasizes just how alone the Byron brothers feel after their shipwreck.
But don't think that Herlong's cutting corners with her choice of title. The sea is also a super-powerful symbol in this book—check out our "Symbolism, Imagery, Allegory" section for more on this briny metaphor.