I would go with the FJ simply because you like it more. You'll take it out more and enjoy it more than the Tacoma.... as long as you aren't worried about it breaking.
I'd suggest giving it a proper once over, new fluids everywhere and maybe a belt or two. New brakes, new tie rod ends, new seals, etc. Basically, treat it as an old FJ you just bought. Then build the rest up!
Now then... I have a quick question. What all issues have you had with your JK? I (knock on wood) haven't had any issues with our '16 JKUR, currently at 75k miles, and am curious what year yours is, mileage, etc.
Similarly, I LOVE driving our Jeep on tips but the 4Runner is realistically more comfortable and is still quite capable. Especially considering we travel like you with a lot of pavement and, unfortunately, only some dirt.