The reference here to the "Valley of the Dry Bones" in Ezekiel may seem paradoxical: after all, this is the sea, with little of anything dry in sight. But the reference has resonance, even beyond the general atmosphere of decay and death Melville has depicted in this story. Bones are mentioned a few times in the text, including when the Bachelor's Delight's longship is described as "warped as a camel's skeleton in the desert" and, more importantly, as the reader learns that the slaves in revolt replaced the Saint Dominick's figurehead carving of Christopher Columbus with the murdered bones of Alexandro Aranda, the slave owner.
In chapter 37 of the book of Ezekiel, the prophet is brought by God to a valley filled with dried bones. God exhorts him to preach to the bones, to bid them rise up and come alive, to re-incorporate with tenons and muscles and skin and breath, which Ezekiel does. The result in verse 10: "So I prophesied as he commanded me, and breath entered them; they came to life and stood up on their feet—a vast army."
God explains himself in the next two verses, saying to Ezekiel, “Son of man, these bones are the people of Israel. They say, ‘Our bones are dried up and our hope is gone; we are cut off.’ Therefore prophesy and say to them: ‘This is what the Sovereign Lord says: My people, I am going to open your graves and bring you up from them; I will bring you back to the land of Israel."
At the very least, the reference is rich with the connection to what the bones say: "Our bones are dried up and our hope is gone; we are cut off." Certainly, this seems true for Benito Cereno, cut off from all hope, as the reader finds him a few pages later.
The full nature of this reference, though, may have two distinct meanings: one seen through the eyes of the Westerners and one through the eyes of the slaves. To the Westerners (including Delano and Benito), the reference may suggest that the slave revolt will be ultimately unsuccessful. That the bones will figuratively rise up (with the help of the "army" of Delano's crew) and restore hope in the system in which Europeans and Americans enslave. But through the eyes of the slaves, alike to the Israelites in their own history with enslavement, this may portend the ultimate wrath of God against the perpetrators of the institution of slavery.