Depending on the current needed by the motors you want to use, you could use transistor-mosfet pairs to drive them from the logic outputs on either the Arduino or Pi.
In the case below, the mosfet(M4) is a XR46000ESETR, the transistor(H5) is a MMBT3904-TP. I use this to PWM control a 12V computer fan for cooling my Pi, although be aware it inverts the logic, so a high signal stops the fan, I have it fed via a 6 channel logic inverter(SN74AHCT04DR), so the code makes more sense to write. If you want to control beefier motors, you could happily power a 12V coil in a relay using that circuit. Include a flyback diode if you do though.