Time of year makes a difference too. Right now tax refunds abound and people are looking for a toy to play with over the spring/summer. I bought mine in the fall and there was a lot more inventory to choose from.
I would hammer down your MUST-HAVES from your WANTS and expand your search area. If there's something very specific you want (like a 5-speed) then try including nearby areas like LA, Phoenix, Flagstaff, etc. or whatever other urban areas are near you. I see 4Runners pop up in Reno that are decent from time to time as well. I though about it and I was thinking, am I willing to drive 6 hours or so for the perfect 4Runner? The answer for me was yes, so I started searching farther out.
I searched for 4 months for a 96-98 with a TRD supercharger. I also wanted a 5-speed but realized finding a 5-speed with a SC was very rare and when they did pop up people were asking way too much for it, like that first post at 12k.