How do I remove this power supply noise?
It seems to happen at harmonics of the line rate. This is showing up as common-mode noise on everything, and because it's AC potential difference between your nominally-grounded body and its local reference it's bound to cause issues with your sensor when your body is nearby.

Where is it coming from? Leakage (parasitic coupling) between the 12v DC-DC primary to the isolated secondary. All line-power supplies have it, good ones manage it better.

As an experiment, try grounding the board to safety (earth) ground to see if the noise goes away. If it does, congratulations, you have leakage. Add a common-mode filter to the 12V or get a better supply.

Another experiment: add a common-mode filter to the line-in on the 12V supply. This would break the AC loop for noise and contain it in the power supply where it belongs.