The only 4Runners to my knowledge that get on the boat from Japan with leather in them are the Limiteds. Everything else ships from Japan with cloth.
However, you can order an SR5 or SE 4Runner with leather. This just means that the distributor will install the leather when it gets to port. Or you can take any 4Runner that the dealer has and get them to install leather. But either way, an SR5 or SE with leather has what amounts to after-market leather. Please correct me if I'm wrong.
In terms of leather recovering, I went with Katzkins. My understanding is that the base model katzkins (quite a bit of vinyl used in the production; backs of the front seats and most of the back seats are vinyl) is what you get if you "order" an SR5 or SE with leather. I got the upgrade level which is mostly leather (I don't care for the way vinyl ages). I did a combination install with some other things, but I could have done the whole install from my upholsterer for $1300. You can find a premium leather katzkin kit online for about $900; you can probably find someone to install it for $400 or so. I can provide links if desired.
I really like the quality of the Katzkins. I went with light gray. It's actually very close to slate colored rather than light gray. Should be a good balance between heat rejection and ability to say looking nice (my experience with light leather is that it gets dirty quickly).
Let me know if you have any more questions. I'm happy to answer them.