I have both, drove the 3RZ auto 2wd for a few years, no issues. I towed a small trailer with some equipment on it, not too heavy, but again I had no issues. I now drive 3.4 4WD auto, for the past year and a half. Fuel economy is lower, power it higher, and with a flow master it sounds cool. The 3RZ has 225K, the 3.4 has 305K, longevity is not an issue with either one. I love both runners and I'd be happy with either one.
So there is no overall best choice, only the best choice for you. If you want a little better economy, choose the 4 cylinder. If you want the extra power, choose the 6.
I also have a 96 3.4 Tacoma with 235K, which feels like a rocket ship accelerating from a dead stop, and I love that too. But I've never had to put a timing belt on the 3RZ! Haha!