Various green seaborne transportation strategies, which minimize the impact of climate and economic losses on shipping, are used in the maritime industry. This study aimed to determine an optimal alternative fuel by measuring and evaluating four alternative marine fuels—liquefied natural gas (CH4), H2, NH3, and MeOH—in terms of sustainability using a multi-attribute decision-making methodology. These were ranked through life cycle sustainability assessments: environmental life cycle assessment, life cycle cost and net present value, and social life cycle assessment. The energy system model showed that in all assessments, the CH4-internal combustion engine (ICE) outperformed the other alternatives. The analysis also revealed that alternative fuel technologies were inferior when considering environmental, economic, and social multi-criteria evaluations. Because CH4 is technologically feasible, CH4-fueled ships have been commercialized and their infrastructure for extraction, storage, delivery, and use have become well-established along major routes. However, CH4 is a fossil fuel, and events such as oil shocks can recur because of regulations in countries with sizable natural gas reserves. Therefore, the technological development of H2-ICE, H2-solid oxide fuel cell (SOFC), and MeOH-SOFC, which are the most suitable technologies together with CH4, is essential.