This particular amoeba is likely present in most freshwater aquariums, especially given the tropical temperatures they are kept. There is another related amoeba species that lives in ground soil and causes a similar infection but has a much lower incident rate than naegleria fowleri. An estimated 16 people die per year due to this infection.
You can reduce the risk by washing your hands with soap and water after contacting aquarium water and ensuring that no aquarium water enters your nose or ears. To date i am unaware of any cases of someone contracting this infection through an aquarium.