Hi Neha, September is still monsoon in both Darjeeling and Meghalaya which means might see a lot of rain and very few days with clear skies. The best time to visit Darjeeling and Meghalaya is March to May (Spring) and October to November (Autumn). Following places can be visited in September - Kovalam (Kerala), Leh, Rajasthan and Himachal Pradesh. For more information regarding places to visit in September - https://www.tripoto.com/trip/best-places-to-visit-in-september-in-india.
Sept end and early oct are the perfect time to visit these places . We visited Meghalaya last year in Oct first week and it was awesome. You can check on blog on the same