I just did this last Saturday. If the marks are light, Meguiars boat polish is a good choice. If that doesn't get them off, I use 3M boat polish and wax. This has a little courser grit, and it leaves the surface appearing a *little* dull if the rest of the boat is very shiny. I follow up with the Meguiars to polish the spot back a high shine.
I got both products at Boater's World.