Try this circuit:
simulate this circuit – Schematic created using CircuitLab
The reason your circuit doesn't work is because you're using an "emitter follower" circuit. Basically what it does is the transistor maintains a voltage at the emitter that is the same as that at the base, minus a diode drop. Using a darlington in this case doesn't help because the transistor will not conduct if the base is lower than the emitter.
Note that the voltage at the collector of the transistor will not be 6 volts when it is on (you don't want that anyway), however the load will have very close to 6 volts across it when the transistor is switched on.
Edit: as mentioned by @jonk, your micro's output pin does not source enough current to drive this transistor enough to switch your pump. You have a couple of options here, you could buffer the output of your microcontroller through a buffer like a 74HC34, or you could use a darlington configuration with 2 2n2222 transistors as shown here.