I have done both blasting and the good ole hard way, manual labor. This not on a FJ40 but a frame very similar. Blasting is great, goes fast if you have the right blaster and compressor. You can also get into all the nooks and cracks easily plus blast the inside a bit. But you will never get the inside completly clean on a box frame. One prob with blasting is you have to clean it up a ton before paint. That means get all the blasting material out of the frame. A real good pressure wash can do this, not much else will. If you don't clean it up after the blast you will have sand all over the place when you paint.
Manual labor is a dirty job but gets it cleaner in the end. This being wire brush, dremel, sanders. If it is real dirty start with a puddy knife and scrape. Then wire brush on a drill or grinder. I find a soft wire brush on a Dewalt angle grinder works good. Then dermil for detail and then sand it starting with some 40grit.
You want to remove all rust so you may find it requires grinding and sanding a lot. A blaster with a coarse grit material will get the rust out too. Once it is clean treat the frame with a rust nuetralizer. Try to get as much nuetralizer as you can inside the frame.
If you can get the frame blasted for cheap, $125 is cheap, then you sure might want to consider that. Cleanning up a dirty, rusty frame is a lot of work. But if you do it yourself you get the rewards of your own work!
Powder coating the frame will be the nicest route. Last a long long time too and takes lot's of abuse. If you go paint I reccomend and industrial type paint such as is used on heavy equiptment or a marine type paint used on ships....even tractor paint is good and any of the three will last a long arse time. Proper prep and priming is important to get your top coat to last.
I am nearly done with my latest frame resto. Just need to do a little welding and then I can paint it. Like I say it is not an FJ40 but is very similar...here is a link,
67 Patrol frame resto