I would have gotten the 04 without a doubt simply because of the lower miles. A lot of people here are hung up on the 4spd vs 5spd, but in my experience, it doesn't mean a thing. I had a Mazda 3 (04) with a 4 speed automatic, then rented a Mazda 6 (08) with the same engine, but a 5speed automatic. On the interstate, both engines revved the same running the same speed. So the final drive ratio was the same for both cars. The only difference is one shifted 4 times to get there and the other 5. The 5 speed may have a quicker hole shot, but when it comes to daily driver cars/SUVs, I don't see the need to even care about that.
13,500 was a good price for the 04, but I would not have paid that for an 05 with 130k miles on it. That is 26,000 a year which is very high. I will not even buy a car used with over 12k a year because that is what the books allow. Most people drive around 15k. This is not to say that a 4runner with 130k is worn out though by any means. If it's been taken care of, I would venture to say that it's only half way though it's life on the engine. Especially if it has been taken care of which most on this site are due to our feelings about our 4runners. But any run of the mill one on a dealer lot, unless I could get it's maintenance history, I wouldn't touch it.