Is your queue line too long? You can go into the ride and change the amount of time that the next boat has to wait. Make sure that there is no max time set: leave that unchecked. You can add more boats: 15 is the default, but you can raise that by going into the cheats and raising it up to 31. Making your station longer will allow more boats to work more comfortably. Usually, I have my wait time at about 5 or 6 seconds.
If the boats are getting lined up in the station while the ride is operating, decrease the wait time. I usually shoot for no more than 2 or 3 boats waiting. Also, uncheck the "wait for 1/2, 3/4 full load.