What kind of method would you recommend for treated sewage effluent injection to monitoring wells?

Assuming that you are looking for biological analysis quite a number of different methods would be acceptable, but try to avoid any artificial turbidity. Use any kind of a sampling method that produces a sample from the well with minimum turbidity. Because biological analysis can be affected by standing water or stagnant water in the well, use some method that allows you to get a sample right from the screen zone or purges the well prior to taking a sample like low-flow purging and sampling would.