The PWM output default to 5V (specifically, it's tied to the power supply, so it may be 5.1V, 5.2V etc. See your power supply). You are able to use 12V pumps successfully even at 5V output. However, you can also use the AUX power connection to change the PWM output.
Pumps that we have used and we like:
These pumps require some assembly to work with the Pioreactor