My rough estimation of the ship books:
Seafarer's is better for high fantasy and quick/easy combat. It also has the best idea content regarding what kinds of things you might see and do at sea along with good underwater content. Broadsides is better for a more realistic feel, historical accuracy in the ship designs, and more tactically accurate combat. It still has fine fantasy content though of course. Seas of Blood, although you didn't ask about it, has the most comprehensive ship ruleset as it is the only one that includes mass combat rules for boarding, however like Seafarer's it is quick/easy rather than tactically accurate ship to ship combat. As an example of the different approaches to ship-to-ship combat, I believe Broadsides is the only one of the three that takes wind direction and speed into account during tactical combat and thus probably the book of choice for people who actually know a bit about sailing and don't want to be frustrated.