Hussar
Legend
While they're 3e books, the rules still work pretty well: Living Imagination's Broadsides!! (for combat) and Pirates (for ship construction rules) are probably the most comprehensive out there. I've used Mongoose's and FFG's rules, but, neither are as complete as Living Imagination's. However, on the downside LI's rules are very tactical, meaning that ship to ship combat is SLOW. However, their ship construction rules are bang on and the treatment they give to ships all the way from catamarans to galleons is top knotch. Since LI's been out of biz for a while though, I'm not sure how easily you can get copies.