I like your September idea, or even early November. I was looking at Halloween last year and I think the decorations stay up for at least a few days after Halloween. July just seems SO hot. On the other hand, you'd get to the parks that much sooner

But it sounds like you really want to do Halloween.
For hotels, I had the same choice-either Courtyard the whole time or split stay.
We're doing a split stay with Hojo/ DLH. It would be fun to stay at DLH especially if it's your last visit for a while and thse pool and slides are SO nice.
I think your son would also like the Hojo waterpark, and they have that nice garden pool.