I followed these three releases pretty closely and waited for all three to come out before I made my choice. In the end I decided on Broadsides, but this might not necessarily be the choice for you.
I chose Broadsides because it is firmly based in realism, which is of strong importance to me. For example, I think that Broadsides is the only supplement that really fully accounts for wind direction and strength for tactical combat. In addition, most of the ships detailed are historically grounded rather than fanciful musings (although there are several fantastic ships as well, like very well thought out air ships and a few submersibles for example). It also has extensive coverage of navigating and piloting the ship. In addition, the ships are all categorized by technological level, which makes it much easier to select groups of ships based on how advanced you want the naval technology in your game to be. This is one of the things that really impressed me. It runs the gamut from old longships to royal galleons and frigates all divided into rough tech classifications. With Broadsides, I feel that I have the ability to create a Moby Dick or Mutiny on the Bounty story and I almost feel like I might eventually have the ability to sound like I know what I'm talking about when I let out the mainsheet or turn hard a-lee.
Seas of Blood and Seafarer's Handbook, on the other hand, are more grounded in fantasy and simplicity. The rules for sea travel and combat are a bit less complex. The loss of realism is compensated by the fact that things move quickly and get to the meat of the matter (the story!), rather than focusing on the real details of sailing. Seafarer's has the strongest section on underwater adventuring while Seas of Blood has a handy system for resolving the mass combat situation of boarding actions. All three books have different strengths. For a high fantasy story where the actual ship is less important than where it's taking you and who's aboard, one of these supplements might actually be the better choice over Broadsides, although I'd be hard pressed to choose between Seas of Blood and Seafarer's if that were my preference. Other folks can give better advice about that.
Note that this opinion is based on skimming through all of them on several occasions but only a complete cover to cover reading of Broadsides, as that's the one I ended up buying based on the skim throughs. I think choosing the book that is best for you depends on how you want to use it in your campaign.