In addition to the Tory said, check your sharkfin antenna and the rear of the headliner... The seal around mine was f*cked and the fin itself was warped upward slightly. During a particularly rainy day I noticed a puddle of water in the rear trunk area and looked up to find the edges of the headliner wet from the rear all the way to around (both sides) to the passenger doors. I did an emergency silicone job and duck-taped a plastic bin over the sharkfin to cover it overnight while the silicone dried.
Next couple of days it was a warm sunny so I kept the windows cracked and ran a fan in there, dried everything up no problem. Did some research and ordered a used tacoma antenna that matched my paint color and installed it. Problem solved.
Anyway, best of luck finding the leak, it definitely sucks having to deal with water inside the vehicle. :/
Here are some pics:
Note the drops of water forming under the antenna nut and connection...
Had to do the silicone in the rain, huge PITA...
To keep the rain off the silicone overnight and hope the wind didn't blow it off:
Rode around like this for about a week, ghetto but it worked like a champ. There is extra in the front because the sharkfin was sort of warped up from sun damage I assume...
And for the record... this is what was inside the nearly empty shell of a stupid sharkfin on mine:
Installed the tacoma antenna with some fresh silicone to ensure it never leaks again
Looks factory!