Use a wetsuit cleaner first, such as oneill wetsuit wash or rip curl piss off. After you kill the stank, try rinsing with fresh water and drying your booties in front of a fan after each session. Just make sure the ankle opening is open to let the air in.
go buy some woolite, its similar to the wetsuit shampoos, but cheaper. you can find it in any food store. mix with warm water and soak em. works for me. getting the boots is dry is key too. i stick a fan on the floor and aim it right towards the insides.
once they dry I like to sprinkle a little baby powder in there. keeps em smellin' fine and makes it easier to put em on.
One funny story, though. One day recently I was suiting up in the front seat of my car with the heater blasting and I lifted my boot up by the dash and for some reason turned it upside down and a ton of powder came out - it hit the heater vent and went right in my face and all over the inside of the car.
Everythying was covered in white powder and I had to open the door to get air to stop coughing. If a cop had come by it would have been a cheech and chong moment no doubt.