@Swedishkiller12 Undervolting a 12V fan on the Pis 5V or even 3.3V pin is not going to give you any benefit. In fact it most likely is going to move a lower volume of air then your 5V fan on the 3.3V rail.
Fan noise really comes down to two things. Air turbulence (fan speed/fin design) and ball bearing quality/noise.
Spinning your fan slower and having an adequate passive cooler on the SOC is likely your best bet.
Have you measured/logged temperatures while under load? If you can do this while running on the 3.3V pin and are staying below the ideal max of 70C (this is not the absolute max, but rather the safe longterm max for most models) then you should be fine.