I run a 4E campaign for two different groups of players on Monday and Wednesday nights, and both groups have just graduated from paragon tier to epic tier. In the Wednesday night game, naval combat has become a key feature of the campaign. I recently ran a battle between two fleets of ships: the heroes' fleet (each player was given a ship to command) and an enemy fleet. The battle played out smoothly, and everyone had a lot of fun.
Here are the rules I used to run the battle:
This ship-to-ship combat system is not a simulation. There's no "facing," for example. It's also simpler than the character combat system because there are no opportunity attacks. That said, I will probably add a bit more complexity to the system over time (rules for combat advantage, for example).
I have a blue-tinted wet-erase battle map that I use to represent the water, and I have card stock ship tokens from the old Spelljammer® boxed set that I use to represent the various ships on the grid. I designed a "character sheet" for each ship so that players could keep track of their ships' hit points and crew. I've attached a sample below. In the meantime, if you're interested in running D&D ship-to-ship battles, I suggest you give these simple rules a test drive and let me know what you think.