I don't know the age of the water heater or if it is natrual gas but it could be the regulator in going bad and admiting too much gas. That would make the flame burn too high and suck the air from the pilot light. A new regulator will cost more than a thermocouple but not a terrible lot more.
Caution: If it is LP gas please call an LP professional. That stuff is very dangerous......enough to blow your house off its foundation.