I have to agree with most here. If you can get a brand new GX460 for such low price - get it!
However, keep in mind, many Mazda dealers also have great incentives on CX-9 Signature as well. Here in the SF Bay area, there are a couple of dealers who will sell you a brand new '18 Signature right now for $40k, so don't look at the MSRP.
As far as driving and what you get with each..... well, like you said they are two very different cars. I have an older GX470 (many people say the GX470 is actually better than the GX460) and an almost new 2017 CX-9 Signature. They are VERY different.
The GX470 rides and behaves like a luxury truck, packed with high quality materials inside and out. It does everything well - it's agile, smooth on the freeway, turns well, parks fairly easy for its size, does not care about the road surface, it is quiet inside, it has lots of room (but not as practical as you would expect), it can tow well and it has an amazing full time 4wd system. Lexus service is the best i have experienced from any luxury or non-luxury car.
It is also a very thirsty SUV. It can run on regular gas but it is still very thirsty. The technology inside it is reliable but outdated. If you are going to keep it for 4-5-6 years, you better be OK to live with this already outdated technology. Also, i am pretty sure, out of the door, with the same amount of negotiating, you will end up paying thousands more for the GX over the CX-9. Again.... Both Mazda and Lexus have incentives, not just Lexus. A 45k MSRP CX-9 can be bought for 40k. Add to this difference the cost of extra gas and you're simply paying more for the Lexus. The resell value on the GX is strong, yes, but because there are so many of them out there and because gas is not getting any cheaper - do not expect miracles. They may not be as hot as you expect 5 yrs from now.
The CX-9, in my opinion, rides and behaves like a large, well put together, high-end sedan. It does NOT feel like you're driving an SUV. Many people like that. I like it too and there is a reason the CX-9 is my daily driver. But i also like the feel of my GX470 when i drive it. It's Very different. The Mazda feels more "gentle" on the road. Smooth ride, quiet ride, very little body roll, sportier than the GX, good power with no drama, modern inside and it very sure footed at high speed. If you are often driving over bad roads or offroad - the CX-9 feels very fragile. You need to protect it. The AWD system in the CX-9 is very basic and not impressive in true off-road conditions. Snow tires are a must with the CX-9 if you have real winters. In the GX - you just don't care when it comes to offroad and snow - it takes it all with no complaints. The CX-9 sits very close to the ground for SUV too. It just does not have the same rugged feel because it was not meant to be driven off-road.
However, for a daily driver, that spends 90-95% of its time over perfect freeways and city driving - I do not need that rugged feel at all. Do you? Simply put, it is easier for me to do my daily errands and handle my daily commute (in traffic) in the CX-9 and have occasional spirited runs with it on twisty roads. It excels doing all of it. I live in CA, so my commute does not include snow or torrential rain. If it did, then the GX gets picked. I also got a great deal on the CX-9 up front, so i am no too worried about the resell value 5-6 yrs from now. Gas mileage is much better too. I use Premium in the CX-9 by choice. I average 22-23mpg mixed driving, with a pretty heavy foot. Same driving style in the GX470 gives me 13-14 mpg. You can do the math.
Good luck with your choice!
