To clarify what Derek mentions, on the sony decks with USB control of the ipod you can set it up to control from the deck or the ipod. So you can do it either way, not just one or the other. Also, again at least with sony, the bluetooth decks do also have usb, so you get the option to hardwire an ipod or use bluetooth. As long as the deck has a unilink input it should also be compatible with sony's marine remotes.
The clarion cz500 also looks pretty nice (4v preouts, ipod, usb, bluetooth) but I don't know enough about clarion decks to know whether that one is compatible with the marine remotes.