An easy way to get the bees out of the water heater would be to slowly fill the water heater with water.  The rising water level will drive the bees out the entrance where they can be bee-vaced.  Unfortunately this will net bees (and queen) only, comb and contents will remain inside the water heater.  Brood will be killed, perhaps when drained again the honey will appeal to robbers, and the drained heater will have a not pleasant biomass inside, but time will solve that.  The water heater should eventually be sealed to avoid a repeat occurence.
 
Aaron Morris - I think, therefore I bee!

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