There is a boat trip that leaves from Harbor Town and goes to Savannah and then returns in the afternoon. We took the trip at the end of May and it was very nice. You leave about 9 am and the trip takes 1 1/2 hours. They will have the trolley meet you on River street and if you purchase the all day ride option you can use it to not only tour but stop and then get back on. You only get about 4 hours in Savannah with the boat starting back around 3pm so you may want to go back by car and check out the more of the sights.
It is the same boat that does the dinner cruises in the evening, but the one we took did not serve anything but drinks and light snacks.
Hope you enjoy.