As well as an online collection of Seamen's Protection Certificates, Mystic Seaport Museum's website has research guides here: Seamen's Protection Certificate Register Database (via Wayback Machine) and a database search: Registers of Seamen’s Protection Certificates.
The National Maritime Digital Library might be useful to get more background information.
Also check Cyndi's List for the category: Occupations: Fishermen & Mariners.