Which is best for pulling a fifth wheel, short or long box?

Another point is that a long box (almost) always has a more comfortable ride (towing or solo) due to the longer wheelbase.

(I say almost, because somebody who has modified the OEM suspension or added air-bags or something will come in and be willing to argue with a fence post about ride comfort.)

ON EDIT: Good point, Bob. I was typing at the same time that you were.