FWIW it may still be the tail end of the rainy season when you are there. If it has finished I'm sure staying on the water will be very nice if you are not particularly susceptible to motion sickness. It should be fine if you are in port or a sheltered area. I myself have problems with motion sickness and even the drive from Cairns to Port Douglas makes me uncomfortable (as beautiful as it may be). Though it could be smooth as glass, in March the trip out to the reef can get rather choppy so some preventative action ain't a bad idea. Contact one or two of the hotels or tour operators up there and ask how the weather is and how it's shaping up.