Not much in the ways of engine mapping for the 4Runner as most are more concerned with off-road rather than on-road performance.
You already know about URD, I'd also check out the BAMuffler exhaust system, and possibly an aftermarket intake (although personally I don't believe they do much). Piggyback ECU's like the UniChip are another -albeit pricey- option.
I'd ask [MENTION=26817]SkylineGTRracer[/MENTION] for his input though, he seems to have the most experience in this arena.
Also, you might want to consolidate all your performance related questions to one thread (maybe this one?) as I noticed you asked about headers and y-pipes in two separate threads before. It'll help get a more constructive conversation going if you make one detailed thread rather than a number of separate, simpler ones.
Tuning is just in name name of the website. They sell exhausts, injectors, roof racks, valves, hardware, etc. All for specific car companies. I am asking if there is a good site like this for 4runners. Like urd?
Try reading through those links I posted for more information.
Theres almost no bolt-on performance mods excluding an intake or exhaust, you would have to either know how to engine map or find a garage that works on Toyotas and have help develop an ECU flash for your runner.
No real sites for performance. You'd have to search here, but you won't find much. There's just no real market with Toyota SUV's in the area of performance unfortunately.