BAttery cables or Alternator...HELP!!!

I need some help. Alright heres the situation, i have a toyota pickup 84 model 4x4. With 6 inches of lift and 36x12.50's. I was out bogging, and i have a snorkel, I was testing out for the first time. I got water 3/4 up the fender almost to the hood. And the engine started running shotty. It could breathe, it just didn't have any power? Well i had to cut it off and pull it out of the pit. After that i checked the intake, the snorkle definately works, there was no water. But later that night my battery died. I jumped it off and made it home. But when I got home I cut it off and tried to crank it back up, nothing. i repeated this process of jumping it off, running it trying to rebuild energy, then turning it off and trying to re fire ,and it was dead as a door knob. I did this a few times.Then I checked all of the terminals and cleaned them, got the battery checked at the part store it was good. It still wouldnt fire. So i tried another battery, same luck. So whats a matter with my truck? I just bought an alternator off ebay for $25 so if thats it im set. Give me your suggestions and any suggestions for waterproofing my engine. I already siliconed the distributer and voltage thing and the points on the motor. What else do i need to do? Please help me?

Places like AutoZone can test your alternator.

appreciate the advise, i dropped my alternator tonight and am going to take it up there tomorrow, i'll let ya know how it goes.....