I have travelled to many European Countries, however, only a couple via Ferry. My trip to Malta was via Pozzallo, Italy, a lovely seaside village in the south of Sicily. From there I caught a ferry and took the 1.5 hour trip to Valletta, Malta. I can honestly say that aside from Sydney, Valletta is one of those cities you must visit by Ferry, it is astoundingly beautiful and great for photography enthusiasts.
Valletta is also a strange city, beautiful from the outside but unlike many italian cities, a little bland on the inside. The actual old city of Valletta pretty much closes down after 7pm, so it is best to stay across the water in one of the suburbs (Sliema) and catch a cheap fast 15 minute ferry to the old walled city.
Malta on the other hand has so many gorgeous seaside villages. I went Scuba Diving in the Blue Hole, Snorkling in the Blue Lagoon and many little boat trips. Camino is a treat and must be on your list.
I rarely recommend tour bus trips but this is one you probably should take over a few days (17 euros a day) and stop off in some of the beautiful seaside villages for lunches and walks.There are many stops on these bus tours. Taxis are also pretty reasonable, but get a white taxi service and get quotes before you agree.
The people are very friendly, not too pushy and the food is an eclectic mix of many cultures (great if you love meat). All in all a great country to visit and I would recommend doing it over one week.