Motor not working via transistor
I believe the netduino IO to be 3V3 and this means the emitter of the transistor can never be higher than about 2.7V with any load connected. This is realistically the problem you have - the motor is only receiving about half of the 5V it needs and is therefore stalling. The led works because it only needs a couple of volts (more than likely).

You need to have the motor and diode (same way round as drawing shows) from the collector up to +5V. The emitter needs grounding and the input to the base (from the netduino) goes via a 1k resistor.