Before you do anything else, pull the batteries out of the boat and stick them on a battery charger to see if you can get a full charge. If you left the batteries in your boat throughout the winter, you very well could have ruined them due to cold weather and not being on a trickle charge over the winter.
Once you've charged the batteries up, put a voltometer on the terminals and see if you're getting 12v. Now put the batteries back in the boat, and if you have a perk switch, switch that to the "all" option or "both" whatever it says. Start your boat up, preferably on the trailer if you have a fake a lake. Use the voltometer to check the voltage at the battery terminals while the boats running. While running, you should see around 13.3 volts. If that checks out, now give the boat a little throttle and watch what happens to the voltage at the battery terminals. It should raise up to a max of about 14.4V. Any higher than that (15-16V range) and your voltage regulator on your alternator is shot. If you see no increase with more throttle, your alternator may be shot.
First things first though, confirm your batteries are charged, and in good working order.
-Mike
2006 Supra Sunsport 20V