I learned from my own research of my seaman/mariner ancestor Charles J. Wagner of Boston, MA that not all Seaman's Protection records, specifically for the 1880's and 1890's, survived, so for the two of us this isn't a good source of data. mine also is difficult to trace through records.
In my pursuit of my ancestor, I got his ship's records from Mystic Seaport, which has a shipping museum that is very happy to send what it has on such things as master, tonage, type of ship, etc.
I also contacted the National Archives who sent me Charles' medical records from the Marine Hospital in Chelsea, MA and his pay records from the ships we knew he'd worked on. It took me 3-4 years of poking around to find where the Marine Hospital moved 1) itself, and 2) it's cemetery, and then when I asked for a check of their records, Charles isn't listed among the burials, but yours may be.
I wrote Massachusett's state archives for vital records, where I found his son's birth record but not Charles' death record, and NEHGS sent me his marriage record but also couldn't find his death record. We cannot find where he died, though we have a date (3 Aug 1894) whether accurate or not only time and successful research will tell.
I've checked out FHL microfilms for various data, and Ancestry.com, finally finding Charles' immigration just last summer. and I've poked in every port I know he was in, to little avail, but no stone left unturned.
And Lloyd's shipping records since he supposedly was an English subject before coming to America (though his immigration has him coming from Germany, and all of the records we do have for him claim he was either from Russia or Poland) so these are some possible directions to look into for seamen/mariner's in your tree -- state and national archives, Misty Seaport, every port you can find record of.
There are also societies for these men. Unfortunately the records for those societies are in document boxes, gathering dust in most places, and you have to go there and personally search the boxes yourself. Since Charles' wife moved her family across the states eventually settling in Oakland, California, no-one is remotely close to Boston or able to travel there now.
Google the area that was your ancestor's home port and then try different terms that fit-seamen, mariner, ships, etc. Sometimes you stumble across some intriguing information.
