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Traditionally, deaths at sea would be reported at the first port reached by the ship after the death. This is true of deaths taking place on passenger ships coming to the various ports of the United States, where a death taking place onboard a ship that docks at New York City would be recorded in New York City.
If the death of your great-grandfather took place while the ship was sailing to a foreign port, it is possible that his death was recorded there rather than in the United States. However, Massachusetts has long recorded deaths of individuals, that resided normally within the state, if the death took place somewhere else. So if you cannot find a death for your great-grandfather, then it is possible that he had moved out of the state before his death happened.
In city directories and newspapers you will often find listings of the shipping companies that were active in a specific city—in this case, Boston. The shipping companies are how you would identify the ships that were leaving from Boston, and are usually listed in the city directories. The dates of embarkation and ports of call for ships were often published in the newspapers, and may assist you in a better understanding of where certain ships traveled, as they often traveled specific routes.