The increasing integration of advanced technology into maritime operations has increased ship cybersecurity risks, especially with the development of autonomous vessels. This systematic literature review critically examines and compares existing threat modeling and risk assessment methods in ship cybersecurity, identifies key challenges, and addresses gaps in the literature. Through a systematic literature review, 25 scientific articles selected from diverse databases were analyzed to understand the evolving landscape of cybersecurity practices for manned and autonomous ships. Significant inconsistencies were observed in current approaches, underscoring the urgent need for standardized threat modeling and risk assessment frameworks that consider the special requirements of autonomous ships. Improved tool support for these frameworks and systematic validation of expert knowledge are also critical. Addressing these gaps can significantly enhance the resilience of maritime systems to cyberthreats.