Stall torque should be similar. The 48V motor will be able to develop more power as the cadence (RPM) goes up.
Having said that, both the 36V and 48V motors have the same thermal limitations, so unless you are doing a cooling mod, you will not be able to utilise the additional power of the 48V motor for very long as it will overheat.
In my opinion get the 36V if you want to run at lower power levels (<400W) on a lighter bike, eg a mountain bike. Get the 48V if you are interested in higher top speeds on the flat and you are less worried about weight.
I use a 36V on my cargo bike, it weights 45KG empty, and the 36V has plenty of torque. I don't need the power as I am only using moderate assist to keep fit. Motor helps accelerating and climbing steep hills.
One other advantage to running the 36V is you can hotrod it - that is run the 36V motor with a 48V battery, increasing its max cadence ... from around 90RPM to 110RPM if you ride with high cadence.