Amplifier volume potentiometer causes voltage offset
Try this... 


Remove R1 the way it is currently wired and all wires leading to it. 
Connect a ~1k resistor from Vcc to the transistor collector.
Connect R1's end leads from the transistor collector to ground, respectively. A larger value for R1 might be a good idea, such as 10k, but it isn't critical.
Connect a 1µF ceramic cap from R1's wiper to the arduino.


Edit:


Also connect a 10k from Vcc to the arduino pin, and a 10k from that to ground. This will cause the output to center around 2.5v, which seems to be what you are after.


This way, the position of R1 forms a "tap" between full signal, and no signal. Then adjust R3's value to give the cleanest output with the loudest microphone signal expected. There is a technical term for adjusting these resistor values - biasing. Also this. Have you calculated what the values should be?