With the colder weather upon us throughout the country, squeaks and rattles are going to be more prevalent. I know you said the noise might be coming from the dash, but check and see if this might be a possibility. The TSB info that I am going to post below might be outdated, actually I really hope it is. It's been out for a few years now, I would hope they would fix it with the most recent years.
By the way, this is from [MENTION=49863]WhiskeyCop[/MENTION]'s thread seen at
http://www.toyota-4runner.org/5th-gen-t4rs/110839-5th-gen-maintenance-documentation-reference.html
Technical Service Bulletins (TSB)
T-SB-0141-10 Upper/Lower Windshield/Rear Glass Tick Noise
If a creak, tick, or rattle noise is heard at the top or bottom of the windshield, or at the top of the rear glass, the source of the noise may be the two stoppers bonded to the top of the windshield/rear glass, or the windshield retainers bonded to the lower edge of the windshield. This bulletin provides the recommended repair procedure to eliminate these types of noises from the windshield/rear glass area.
As for squeaks, any of the newer 4Runner's have the dead pedal squeak (left of the brake pedal) during the colder weather?