You will still be able to hit 'a' waterpark, though most likely not both of them. Disney generally closes the waterparks for refurbishment in the cooler months, but one always remains open.
October
may be less crowded, but probably not much. The Food & Wine Festival is in Epcot in October which makes that park more crowded, particularly on weekends. Also Mickey's Not So Scary Halloween Party (MNSSHP) will be happening in October, which is another big draw. It is a hard-ticket event (meaning you have to purchase a separate admission) but because it's so popular many people travel to Disney at that time of year just to catch it.
We visit Disney every fall and our personal preference is to arrive at the end of September and stay through early October. This time usually falls in a gap between the end of the free dining promotion and the beginning of the F&W Festival and MNSSHP, and we feel it's been the best option for us as far as crowd levels go. It also lets us to catch a Halloween Party and a day or two of the festival just before we leave, giving us some of the fun and less of the commotion associated with the two.
Food & Wine is an especially great time for a homeschooling family to visit Epcot. Besides all of the great educational experiences that are normally there, during F&W there are many more countries coming to set up booths and displays, so the cultural exposure is multiplied several times over. And because those countries are represented by natives and not just American employees, your family will have the opportunity to learn a lot. If you're not already familiar with it,
www.themouseforless.com has a great section for educational experiences at Epcot. Visit the 'downloads' section and then click on 'just for kids'.
Have a great vacation!