I have a 2 stroke Yamaha 90 because my older boat has a heavy rear end with the gas tank across it plus the kicker motor and I needed the lightest possible motor.
However, if the boat is designed for the additional weight of a 4 stroke, I'd definately go that way because they are much more fuel efficient, they are almost silent and they don't stink when idling. At over 2 bucks per gallon, that will add up!
Mark