Ares Games recently released Sails of Glory, a Napoleonic naval counterpart to Wings of War/Wings of Glory. This series' game mechanics are the inspiration for Fantasy Flight's X-Wing. Here's a Sails of Glory community website:
http://www.sailsofglory.org/content.phpUkrainian company bombatgame recently released a fleet action board game called Admiral:
http://bombatgame.com/en/products-page/Zvezda (renown for its 1/72 plastic sets) has also recently released a naval wargame based on its Art of Tactic series:
http://www.the-ships.com/eng/If you want to go the more traditional wargaming route, there's a few options here and there. Langton Miniatures makes a Napoleonic ruleset, Signal Close Action, and an ancients ruleset, Naumachiae, to go with their ships;
http://www.rodlangton.com/If you don't mind looking around for something that's a bit OOP, you might want to consider the following Games Workshop games: Trafalgar (a Warhammer Historical ruleset for Napoleonic naval warfare); Dreadfleet (a Warhammer Fantasy boxed game); Man O' War (a Warhammer Fantasy wargame); or Battlefleet Gothic (a 40K wargame). There's also the now-defunct Pirates of the Spanish Main (and subsequent series), a collectible game that uses cardstock ships. Careful not to confuse it with its card game successor.
I was shopping around for a satisfying naval game for a long time. Even with all the options I mentioned above, I couldn't find one that really stuck out as being thematic, affordable, understandable, and aesthetic.