Seafoam is absolutely fine to run in your boat. I personally think it makes the boat run smoother. I usually buy the generic version because its cheaper (Rural King, Menards, Wal-mart, etc..) I know a 30+ year boat mechanic who swears by it.
However, if you know you are going to run your boat for several hours on a given day, you might try Berryman's B12. Now that stuff is a powerful and relatively cheap.