I was/am in a similar state, although I have addressed it for the most part. Rust isn't something you can just wave a magic wand at and let it be gone. Let me give you some tips, also, post a few pics of the rust.
1) Take a large mallet or large hammer and get under the car and start wacking the frame with it. It feel solid when you hit it, almost like you're hitting a gong where it wants to reverberate. If it sounds soft or you feel like you're going to dent it, then the rust there on the interior is significant. You will want to start making a mental note of how bad it is as you go along. If there are a lot of areas where you look at it and think "this is really bad, this may not be safe to drive" then just swap the frame if you can do it. You can still buy a whole frame from Toyota for ~4k. Yea, that's a lot but it may be worth it. You could consider hiring a welder to weld areas that are really bad but I'd advise just getting a new frame. I myself, am contemplating it but I probably wont since my rust has been addressed and isn't bad. I trust my frame enough to carry around my 2 year old if that says anything.
2) If you determine that most of the rust is surface rust and your frame is solid still, then do this:
start scraping the rust off underneath using a drill (portable probably best, but if you have one that has a nice long cable then that works too). Attach to the drill this kind of wire brush...
Amazon.com: DEWALT Wire Brush, Knotted, 1-Inch (DW4902): Home Improvement
Amazon.com: Katzco Wire Wheels Brush - 2 Pack Knotted and Crimped Cups for Rust Removal, Corrosion and Paint - Hardened Steel Wire for Reduced Wire Breakage and Longer Life: Home Improvement
I linked two, but the key here is that twisted wire adapter. The other adapters are TRASH, dont buy them. Won't work for what you want to do and you'll just ruin them.
You're going to get under there and spend a freaking week taking off as much rust as you can until you see some shiny metal. Another item that is awesome for this, is a needler. Rent it if you can, it will just knock that rust right off and gets in some tight spots. Just gotta be careful with a needler when you're around brake lines and such. This process will take awhile and will be exhausting but it is required if you don't want to just swap the frame.
What this wont do, is get the rust on the interior of the frame... BUT.. a large mallot... wacking the frame all over will knock that rust loose really good. Then you will want an air compressor to blast the rust out the drainage holes.
Don't be lazy, take your time with all of this. I spend about 5 days under my truck for 4-8 hours a day just cleaning the rust out.
Once you get the rust away down to as much shiney metal as your forearms can bare, it's time to start using some products on them.
First, I suggest spraying your whole frame with a degreaser such as GREASED LIGHTNING. Buy a gallon:
Amazon.com: Greased Lightning 204HDT All Purpose Cleaner/Degreaser 128 oz (2 pack): Health & Personal Care
You can pour it into any spray bottle. Spray the whole frame inside and out as best you can. Go overboard. SPRAY THAT SHIT GOOD. As you're spraying, get some of those large green brillo pads and wipe it around as best you can. We have to remove as much grease and grime as possible before the next step. This is a very important step, you don't want that crud on your frame when you try using a rust converter.
After you got it all sprayer and have wiped it down, hose it down. Rinse off the greased lightning... THEN DO IT AGAIN! Yes that's right, do it again.
After you got the second round done, it's time to use a rust converter. I suggest using Corroseal.
Amazon.com: Corroseal Water-Based Rust Converter Metal Primer, Rust Converter - 1 Gal,82331: Industrial & Scientific
You could also use OSPHO.
Amazon.com: THE SKYBRYTE COMPANY 1275 OSPHO GAL Metal Treatment Coating, 1 Gallon, Green: Home Improvement
But I prefer Corroseal. Both work, OSHPO is a little runny so it's hard to keep it on there. IMO, OSPHO would be better if you can dip your frame in it but you can't.
The key to corroseal is to use a SPONGE. Like a sponge you'd use to wash your car with. Get a couple sponges since they get dirty fast. Corroseal will convert surface rust to an innate metal and then coat it. You will have to coat the frame with corroseal 2-3 times but in the end it will be nice and shiney and resistant to water.
That's it, it will take you awhile to do all of this and I would only do this if you're able to leave your 4runner jacked up at least a foot or more for a few days and have all the necessary tools and time. I check my frame bi-yearly after doing the above and it still looks really good. There are areas on my frame where I can see that I didnt remove the grime or rust good enough, and the rust continues to grow underneath the corroseal layer. So I just grind it back down in that spot and repeat the above steps on that spot. It seems to be doing very well now.
The key is really getting that current rust off it. Remember you'll never do a great job on the interior rust of the frame. I do jsut spray the corroseal or OSPHO on the inside of the frame occasionally just to try and slow the rust down. It works.