How to use 2 power supplies in my scheme?
The usual procedure I use for motors is through a H-Bridge. But since a vibration motor isn't bidirectional I believe we can use just one switch in the following configuration. (I'm assuming its a 3V motor).



Instead of the D3 pin used on the arduino you can use the GPIO pin from the RPi. Furthermore you can also use the 5V output from the Raspberry pi for testing, otherwise i usually like to use an external battery for this.

Source for further reading: 

http://learningaboutelectronics.com/Articles/Vibration-motor-circuit.php