I agree to take them out. I would keep them in a simple setup and keep the water clean. I would only treat if you see signs and sypmtoms of infection. Be very careful of Fish meds and remedies...most are toxic to newts. I have found all types of remedies and concentrations to be just a "roll of the dice". Cooling them down for a week or two sometimes helps.
I would totally nix the old set up. Dispose everything in the tank that can not be disinfected (live plants, filter medium, etc.) Redo your set up and get the filter going again. It will take a while to build up your filter's bacteria levels (may use starter solution in fish stores). I would not put the newts back in the the new setup until the filter has been reestablished, since ammonia levels can be high in new setups and will just make them sicker. You need to look at the temperature of the room your keeping them in as well as the light source. You want to stay with in the high 60's-low 70's and not in front of a window with direct sunlight.
I don't know how long you've had them, but don't beat yourself up. If bought from a pet store, they probably were already infected. I've had seen this a lot with pet shop purchases. I have also had diseases pass through live food sources as well.
Good luck, keep us posted.