My FIL drives my 99 4runner right now. He had me sit in it the other day to hear a sound coming from the dash. It sounds like there is a fan running under the dash all the time. Not under the hood, but inside the dash. When you turn off the A/C you can clearly hear it.

Any ideas at what this could be?

 

I do not know if the '99 is the same way, but I had a similiar noise on my '98 and the kids had turned the fan on for the backseats. It is still new to me and I had forgotten it was there.

 

that would be my guess as well.

Maybe get us an audio sound clip if that is not it. Sounds are tough to diagnose by description over the internet.