If you have a choice I would go with 1000 rpm. It will run a little smoother as you raise and lower the mower, and consequently change the shaft angle. 1000rpm may cost more because you need a more precisely balanced PTO shaft, but it doesn't need to be as heavy - so could be a toss-up. It should also save a little power because the transmission only has to step the speed down about 2:1 instead of 3.7:1.
My dad changed his silage blower from 540 to 1000rpm with a kit that added a step-down gearbox to keep the machine running the same speed. One interesting change was that when it plugged it would kill the engine instead of breaking the shear bolts as it did before.(exact same tractor)
ISZ