My son and I were just at the Animal Kingdom Lodge in the latter part of September, and we had no concerns whatsoever with housekeeping and the cleanliness of our room. It was cleaned in a timely matter (much better than our experiences at the Grand Floridian), too.
I also looked at the reviews at TripAdvisor which allows guests to rate their experiences at resorts on the following qualities: pool, cleanliness, rooms, service, and value. Of those 5 qualities, it ranked highest in cleanliness with 4+ stars. I will share with you that there is construction going on as Disney Vacation Club building are being added to the resort; you may hear some noises during your stay.
I wouldn't hesitate to stay there again! The magic of the resort with its incredible theming, rich aromas, and amazing views of the savannas make it a wonderful experience for us.