The Wildebeest Migration in September is still more active in the northern part of Serengeti and Masai Mara. The Herds are still within these areas as they keep feeding into the short grass available. However, you will notice a decrease in the number of herds since some will be moving back to Serengeti from Masai Mara.
In September, you should visit Northern Serengeti as they will all be around this part as they congregate to move south. Huge numbers can still be witnessed in this region, as well as active river crossings in Northern Serengeti.