Unplug it, drain as much water as you can, and let is sit out for a week or so to be sure the insides are dry. If you have another airpump that can replace it for now, use it. Also, you need an inline check valve to keep water from backing up into your pump. Somewere between the airstone and the pump, on the outside of the tank, cut the airline and plug each end into the valve, but be sure that its flowing the right way. Check valves are one way, so be sure its pointing from your pump towards your tank along the line. Once it is installed, it will keep water from getting sucked back into your pump.
Either that or set your airpump higher than your tank so gravity can keep the water down away from the pump.