Both places are popular spa destinations. And both will be warm in September, but that also means you can probably get some deals. Rather than pick a city, do some research on the spas. Consider your budget, desired services and additional plans, wants and needs. Both cities offer plenty of options for outside social activities and nightlife, etc. but the spa itself is probably the best place to start.
I would recommend JW Marriott Camelback Inn or The Phoenician. Both have wonderful spas. Camelback Inn is more southwest in atmosphere and has been a part of Scottsdale history for many years. The Phoencian is newer (80's) and more classically upscale, and larger. It's restaurants are all good - several to choose from on the property. Either one is a short distance to Old Town Scottsdale for nice shopping and more dining options.
Another good one is Fairmont Princess. Willow Stream is a fantastic spa. Just be sure to get one of the updated rooms (I think the renovation is complete, but don't remember for sure.) It is located further north and will be near Kierland Commons shopping area.
Good luck with your decision.
I agree with both Redrox and Aztchr....
Check into all of the spas themselves, as this seems to be your focus, then go there. Aztchr's suggestions in Scottsdale are excellent.
A few additional suggestions:
1.Check out Sanctuary, they actually have Spa Casitas which are amazing. Sanctuary is one of those places that is a unique resort that I don't usually suggest, but your trip is exactly when I would. It is a very private oasis.
2. Mi Amo in Sedona. is actually a destination spa and is rated #1 Spa resort by Travel & Leisure. For your trip this would be perfect.
Check these out, for a spa trip they are top of the list. But again, the other suggestions are the best in Scottsdale proper.
One last note..I live in SoCal, honeymooned in Palm Springs, and vacation every year in Scottsdale.
Both are similar settings, but Scottsdale is much more of a city and PS is more desert community. And as far as spas go there are probably 8 to 10 in Scottsdale that are heads and shoulders above anything in PS. I love PS dearly and could suggest some very cool places to stay that are classic mid-century resorts. But as far a spa stay, I would definately say Scottsdale.
Don't know if you are all set by now, but ...
If I had to choose just between the two places, I have to admit I prefer Palm Springs.
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