November is much better for weather. It's warm, but not as hot or humid. September is still basically summer, so you have the threat of hurricanes and afternoon t-storms (though your late September dates will have lower probability than if you were there closer to Labor Day). We went to Orlando in early June last year, and it was like walking on the surface of the sun, and afternoon thunder rumbles meant temporary ride closures. November CAN get quite warm - or rather chilly. We were there in early November 2018, and it got into upper 80s, but that was apparently a slight anomaly. I've also read reports of being being surprised by unexpectedly cool weather, so bring some layers.
But September will be much better for crowds. Although there's no true off season at WDW anymore, late August and September are lower crowd times. If you are people who like personal space, and enjoy taking in the little details of Disney, then September is a much better time for being able to appreciate the imagineering that goes into the parks. September is also much more likely to have discounts.
Both of your times will be during party season, with Halloween parties in Sept and Christmas parties in Nov closing MK early. Personally, I think early MK closures are fantastic days to visit, because MK has such nice low crowds earlier in the day from people wanting to save their MK days for a "full" park day and see fireworks.
You can have a great trip no matter which time you choose. In November, you will probably be better able to power through a whole day, but the larger crowds will mean you want to get good FP. In September, you might want to do mornings at the park, take an afternoon break (bonus - you know it will always be swimming weather), and return to the parks in the evenings when it's cooler.