Jennifer,
I have always considered September the single best month to visit Walt Disney World, largely because of what you just said. Crowds are smaller because most families are "in school" during that month. But I also like it for the summer-like weather that is a bit cooler than the July/August blistering heat.
As for water parks, they are both great, regardless of the makeup of your group. But if forced to choose, I would recommend you go to
Typhoon Lagoon for the following reasons;
- The Beach and Surf Pool area (it makes your trip more like a Florida vacation if they get some 'beach' time)
- The Shark Reef (a fun snorkeling area that is exciting for younger kids without being dangerous)
- Ketchakiddie Creek (an area reserved just for kids under 48" tall)
If she is an "older" 6, I would then revert to
Blizzard Beach, which has two separate kids areas, one for little kids, and one for pre-teens called
Ski Patrol Training Camp. But probably you will find that Typhoon Lagoon is the best choice, for the reasons above.
Have a Magical Vacation!