Several other people have added things to the list that I have and have used at times in the past..
Isle of Dread (original) - also I just got dungeon 114 and that had a good amount of info for use in it.
Ship of Horrors - played it back in the old 2E ravenloft period
There are also several good articles in Dragon over the years and if you know someone with the archive CD you should be able to find them. I have too many dragon magazines to count, and did not have time to try and find the issue numbers but one of them had the mariner NPC class in it.
I am also looking at getting the PDF versions of the "Evil Tide" series for material to be used in my game. I have not seen these before, but at 4.95 as a PDF it is worth my time to look at it.
Also, if you use visual props take a look at WorldWorks.
They have a PDF for constructing a whole island landscape and a Galleon, and the sets look really good. I am planning on buying them as soon as the cash is available.
The Swashbuckling Adventures series (AEG) also has quite a bit of nautical rules and flavor spread throught the material, and the Kingdoms of Kalamr Player Guide has a decent Pirate class.
If I think of more I will pass it along.