The last one is the one that sounds the nicest. Doesn't mean it is right but I would never ever write the way the first two have it.
As for why, I think it's just the proper ordering:
The driver took for a ride the people who had been waitingYou don't "take for a ride the people." This is like, straight up Yoda speak going on here.
The driver took the people for a ride who had been waitingThe "who had been waiting" left out at the end is awkward. Because you can just end the sentence at: "The driver took the people for a ride," and it sounds fine then all of sudden these extra words come tumbling in and it gets weird.
The driver took the people who had been waiting for a rideConnecting the 'who' directly to the 'people' makes more sense. They were waiting for a ride. Who? The people.
I realize this is not a very pragmatic way of explaining this, so someone else with knowledge of how to use "modifier" and that sort of jazz should probably come in and explain. But for me the choice is quite clear even if I can't articulate the reasoning very well.
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