No passenger ferries offer service between Miami and Nassau, as of 2015. Discovery cruises has offered day trips between the two ports in the past, but that service ended in 2011.
It's possible to take ferries from Fort Lauderdale to Nassau by connecting in Grand Bahama Island. Bahama Ferry Express offers service between Fort Lauderdale Port Everglades and Freeport, Grand Bahama. Passengers can then continue to Nassau with Bahamas Ferries.
Another option in lieu of a ferry is to charter a private boat. Many cruise lines offer trips between Miami and Nassau, but passengers are discouraged from disembarking before the end of a cruise.