The Vaporretta (waterbus) goes from St Marks to the cruise ship berth. Some one will come up with the exact name of the 'bus stop' at the cruise berth.
This site tells you how to do it:
We did the same cruise last year and stayed in venice 3 nights, we gotthe water taxi from San Marco square it was really easy we just asked for the cruise terminal when we bought are ticket and told us which stop to go to. it took about half an hour, we were told not to board till mid afternoon but left early and we boarded about 11.30 couldnt get to our cabin till after 1 but they took our luggage. we had a fantasic week im sure you will.
We walked to the terminal. Just head for the Place de Roma(sp)and it took us about 1/2 hour or so. If you don't fancy walking with your cases a water taxi or bus would be your best bet. Enjoy Venice, one of my favorite places!.