Welcome to the DLR DIS boards! 3 nights is enough to see most of the highlights and some of the lesser attractions, but you will not be able to see everything at a reasonable pace, especially in those months (explained later). First, here's a thread that is super useful in WDW vets planning a trip to DLR, written by our wonderful Hydroguy!
http://www.disboards.com/showthread.php?t=1162599
As for the two months mentioned, you have pros and cons with each. Both months have about the same weather, maybe slightly nicer in June. It's not muggy, but it's nice and warm all day. Both times are less crowded than the busy summer season, but September is usually the least crowded month at DLR in general. Both will probably have rides down for refurbishment (although the new World of Color show in DCA will be running by then) and during the week in September I'm pretty sure they don't do fireworks/Fantasmic/WoC, but I don't know if those are important. Also park hours: June will have much longer hours during the day (obviously because there are more crowds), but even with crowds, longer hours make a huge difference in the amount that you are able to do. Just some things to keep in mind.