The Air Asia check-in counter closes 45 minutes before the scheduled departure time for flights to KUL. If you're checked in, you'll make the flight, even allowing for time to clear immigration (barring overstays or other issues with your passport/visa/etc.). It's a small airport with maximum walking time to the gate after immigration being about 5 minutes. The issue would be if you didn't make it to the check-in counter before it closed, and you can attenuate a bit of that by doing web-check-in, though you still need to approach the counter for passport check and baggage tagging.
Private boat hire is prohibitively expensive (more than 10K THB).