Make or buy a cheap g-meter. I think you can get pretty cheap ones that just tell you if you exceeded say 30g or whatever the one is rated for. they are just glass tubes in a sticker and the tube breaks after so many g's. Look at the G rating for the hard drive you intend to use and make sure you don't exceed it. I would be willing to bet that if you mount the hard drive rigidly to the wave runner that you won't have problems with it. Check out this hdd.
http://www.hitachigst.com/hdd/support/5k100/5k100.htm
300/160G operating shock rating. No way your experiencing 300g when your riding. You might get up to around 40 or so if you hit really really hard. I'd go with a laptop HDD.
By mounting your hard drive rigidly to the waverunner you're allowing the drive to take on all the momentum of the waverunner. G force is caused by acceleration and deceleration. Momentum is the ability of an object to resist these accelerations and decelerations. If your drive has a lot of momentum, it will be more difficult for it to experience a lot of G-force.
Drop a car from 5 ft and it experiences maybe 20 - 25g's. drop a hard drive from 5 ft and it experiences say 400g's. Mount the hard drive rigidly in the car and it will experience the same force as the car. Same principle with a waverunner. Water gives a little, allowing a relatively slow deceleration of the waverunner and everything attached to it.
The only other issue is vibration. That could really screw a drive. If you think it's going to be a problem, mount the HDD with firm rubber between the mounts.
mounting with stiff rubber is about the best you can do with a hard drive.