I agree. Your fuel filter would not be allowing water to get to the air box, since the two systems dont really connect until inside the cylinders. If the water is on the dirty side of the filter (towards the fender) then I would recommend not hitting big puddles anymore... The inside of my airbox is caked in mud on the dirty side haha. If it is on the clean side (towards the motor) then i would replace the air filter and make sure it is making a good tight seal.
If that does not do the trick, then start checking the tube for leaks. Do you have the stock air intake or do you have a cold air intake?