1. Use Cars.com or something similar to find exactly what you want.
I found that if a dealer had to order or trade for the vehicle that I wanted, they were unlikely to work with me very much on price. On the other hand, if they had the exact model/options/color combo that I wanted on the lot, they knew that there was a greater likelihood of making a deal. Still, you don't want to seem too eager to buy
2. Purchase through a high volume dealer, if possible.
I'm from Central KY yet it was worth my time and trouble to fly to DC to get exactly what I wanted and at the right price. I have never seen a dealer do as much volume as Koons Toyota in DC. According to their website, they have 70 4Runners on their lot, seemingly priced below invoice. I'm assuming that they depend so much on selling volume that they're willing to take a hit on the sale price in return for a higher hold back or bonus from Toyota.
I was able to get my blue TE Premium w/KDSS for $37k. Not the lowest I've seen on here, but certainly on the lower side of the spectrum. It beat any Costco or TrueCar price, as well as any other dealers' offers by $1500.