For all of these you need to realize that the maximum you can spin a propeller is around 3000 RPMs (exact speed depends on the diameter of the propeller) before the tips of the blade reach the sound barrier and the blade becomes inefficient.
GPU - Ground Power Unit, made by continental to operate air cooled generators for the military. Were well made. Some had one mag and most of those are converted to 2 mags., and some had 2 mags. Is fairly cheap for a starter motor. Lighter weight due to air cooled. Produces more torque per RPM than automotive motors. Many of them out there, there are beauties and there are turds. Many have lots of modifications and run like all get all. I have never operated a boat with one yet, but have been around military GPUs. We ran regular gas in the generator I knew.
Aircraft engines - mostly talking about Lycoming and Continental air cooled motors that were made for aircraft and certified by the FAA to be used in aircraft. Most used in airboats are from prop ground strikes or have something about them that makes them unable to be used in aircraft any longer due to FAA rules. Some use regular gas, but most run on aircraft fuel. Tend to run hotter on automotive gas, and low octane can cause problems with predetonation. Sizes from about 140 hp 4 cylinders to the beautiful 0-720 Lycoming producing about 400 hp. Most max out RPMs at around 2700-3000 and run direct drive, no reduction gear. Some are fine machines and some are junk. Parts tend to cost alittle more due to the words AIRCRAFT PARTS.
Automotive - you name it, probably 350s are the most common, with lots of others like 454s, 502s, 383s, as well as custom engines. Most of these produce peak power at over 3500 RPMs, so they use a reduction gear drive unit to allow the motor to reach peak performance without over spinning the propeller. Some run on regular gas, some only on premium gas. Parts of some are more common, cheaper, and more people tend to know something about them. Tend to be heavier, are water cooled, very common in airboats. Some set ups produce lots of HP with smaller motors, but the person that builds it had better be good. Like all the others, some are fine and some are anchors.
It is a choice of preference, what type hull and size are you buying? What do you plan to do with it? (I worked in the seismic field for a time, there is no way a Lycoming would have taken the abuse I gave those motors. Foot in the carb., 4200 to 4900 RPMs all day, Propeller is going about 2100 to 2400 for an average of about 5 to 7 hours straight everyday of the week, 500 to 800 hours in a summer.) Are you going to cruise water or run land alot.
We cannot tell you which is the best for you. The best way is to find someone and ride with them where you plan to go. See what seems to run best in that situation. Guest loves his 4 cylinder lycoming, others love those 502 monsters. Only experience will tell. But starting slow is the best and a good GPU is the cheapest set up around.