I have been noticing my carpet is wet in the rear driver side corner everytime it rains decently hard. I believe this has been happening for years but it seems its getting worse. I am about to put 4 15 inch subwoofers and I'm really worried that I'm only going to make that problem worse, and I have MDF in the cargo area. It is not leaking from the roof which makes me think its the taillight but I have been looking into and see that it could be due to the sunroof drains. I was able to record where the leak is actually coming from sorta, to see the real location I would have to take off the side interior panel in the cargo area above the wheel wells, which I will most likely do when its dry next. I am going to try and attach the video below. nvm forum doesn't support videos, so here is a YouTube video.
Has this happened to anyone and does anyone know the solution?

4runnerleak - YouTube

Check out 15:20 mark in @mtbtim vid.

I also suspect the sunroof drains. Start there by cleaning the drains and then try and see if you can get it to leak by spraying all over the roof with a garden hose. If not then you are good.

There is a vent in that location that allows air to flow in/out but I highly doubt that would be leaking in the rain unless you're in some sort of parallel universe where the rain falls in reverse from the ground into the sky.

Definitely looks like it's coming from the tail light. I'd replace your tailgate hatch weather seal and tailgate window seal. Make sure to check for dry rot on existing seals. Water will follow the path of least resistance and the leak will only get worse over time.

turns out it was the rear driver side cargo window seal, I dumped water over the window and it started leaking inside. there's a little gap between the metal and the window I wonder if I could just squirt some silicone in the gap to fix it. rather not remove the window.

Glad you found the source of the leak. Personally, I'd pull the window/seal in case you have trapped moisture causing a buildup of rust and common crud which could ensure worse problems down the road.

Hope this helps: Side Tracked | 3rd Gen Toyota 4Runner Rear Quarter Window Removal - YouTube

Ha, that could have been my backyard 6 years ago. I was dismantling 4Runners in my RV pad in the backyard just like that dude is. I will say, the rear quarter panel windows don't always play nice when you try and remove them. In fact, I have never successfully removed one. I was selling them so after cracking several of them I stopped trying as no one wants to buy a broken window. Be prepared to buy a new one if you give it a shot. I would try and seal from the outside first before trying to remove.

Great advice! Duly noted in the PITA column (Pain in the a**), for future reference.