You would be better to use a 12V fan.
The 5V is for powering logic. It should not have motor loads, even fan motor loads, applied to it. You will not be saving power over using a 12V fan. According to @Tom 's answer, the 5V is derived through a linear regulator.
A linear regulator has the property that the current drawn from the regulator at 5V will equal the current drawn by the regulator at 12V. $7/12$'ths of the power will be lost in the regulator chip as heat, which may cause the chip to overheat if there is not enough cooling margin in the thermal design.
If you use a 12V fan the current consumption of the fan for the same cooling capacity will be lower, and you won't waste more energy dropping the voltage.
May I ask how hot the steppers are? Too hot to comfortably hold for more than a few seconds may still be completely acceptable for motors. So hot that the plastic holding them melts is too hot for the mounting, but may still be ok for the motor. So hot that they cause burns with 5 second contact is probably too hot.
If the motors are too hot, it might be better to check the current the motor drivers are programmed to deliver (either through software configuration or a potentiometer -- I don't know the printer). Getting the current right is a better fix that managing the excess heat. It may also improve the linearity of microstepping and improve print quality.