what would be the lowest refrence voltage you could use with out the noise effecting the ouput
1.000.000 volts will make most noise not show :)

noise will always "affect the output", the question is not "if", but "how much"

anyhow, to clarify, the higher the reference voltage, the less you will see noise affeting the reading, just visualize:
for an 8 bit ADC
if Vref is 256 mV 1 mV of noise will change the reading
if Vref is 2.56 V it will take 10mV of noise to do the same

for a 12 bit ADC
if Vref is 409.6 mV 0.1 mV of noise will change the reading
if Vref is 4.096 V it will take 1mV of noise to do the same

Erik