How to reduce noise in SMPS (Switching mode power supply) circuit
For the Boost convertor like other convertor you have output ripple and EMI. 
For output ripple reduction the best way is adding a good CLC filter. 
Increasing the value of C12 and C16 could have direct effect on your output ripple.
For the EMI reduction adding an Snubber RC circuit over the D8 diode or from its anode to ground is also a good practice. Reducing the switching speed of M3 also has direct effect on the generated EMI.

Please look at the following document:

http://www.westmichigan-emc.org/archive/SMPS_Teune_Mee.pdf

Texas Instrument document "slva790" is also a good guide for EMI reduction.