Depends what you want really - a good boat trip ( like the Sami Star from Sami ) will take you to Vathy ( Ithaca's capital ) and Kioni. If you take the car ferry it will give you the chance to explore more of the island. There is plenty of accom on Ithaca but it would be wise to book if you are going in August as that's when most mainlanders visit and accom will be scarce. The northern part of Ithaca has the lovely towns of Frikes and Stavros.
Ferry takes 30 min or an hour from Sami - depends on which port you dock at.