Placing in a container with sufficient water and then freezing is, to my mind, the most certain and humane. The fish is unconscious long before the dropping temperatures kill him. Another method, although less certain with larger fish, is to add carbonated water (i.e. C02) to the water in a container untill the fish loses consciousness and then suffocates. Other methods using sedatives, etc. are also recommended. Chopping off the head with a knife, or smashing with a hammer, are also feasible, although a bit messy (but from the perspective of the fish, relatively quick and painless, especially compared to flushing).
Regarding your ammonia and nitrites, you say that they are "down". Down from what? They should read zero if your tank is properly functioning. Please clarify.