Vinegar is the best - and safest - cleanser. Just soak the filter and a mild solution, and also use it to clean your unit, inside and out. There is also a bacteriostat solution avialable for prevention of future problems. You should be able to find it the same place you got your unit. If not, places like Walmart or Lowes should have it.
This could also be a warning sign of an inuculation problem in your home, and a liberal spraying of Lysol on all surfaces while noone's home should be able to help knock it down. (This should probly be done around the same time as a professional hvac unit & duct cleanout if one hasnt been performed in awhile. They can also spray these areas for mold and fungus.) :]