I want to use a netti pot but am scared of the water having amebas. How can I make sure my water is free from them?

Boil your water. If you are concerned about pathogens in your water supply, simply boil your water on the stovetop or in the microwave for 5 minutes, then allow it to cool to room temperature before using it as part of a neti pot treatment. You may have heard about the 'brain-eating' amoeba, "naegleria fowleri", infecting people via water sprayed up through the nose. Your risk of catching this is very, very low.
In the US? If you are in the US and use city water, it is unlikely, well water or pond water has a remote possibility. If you boil the water first it would clear any amoeba, so that would provide you with assurance if you have any concerns, or use bottled water.