Lets see some pictures!!!
Boulder Toyota is cool, they have sold me TONS of FJ40 parts. I usually go there first. Non OEM can be sourced from places like NAPA for certain things like Matt says. Then for others you've got the MAF, SOR, CCOT, bunch as others have mentioned. I try to avoid SOR due to their high prices on shipping and parts. MAF and CCOT have their own demons as well, but when it comes down to it they usually have what you need and are cruiser people. I haven't tried Crusier Corps but probably will.
Used parts are the variety of FJ40 Junkyards around. Salida Classic Cruisers, cruiser parts.net All the used places you'll have to be careful about what you think you are getting. remember these things are old and most used parts will be as old and rusty as what you are trying to replace.
what year is it?