Nice plot. OPs main problem may be that he does not know what kind of noise/disturbances he has on his signal. And what I understand, he doesn't even know what is the signal he is interested in (how dynamic the system is).
You need to know the system. What is the switching frequency. What kind of output filtering the PSU has. What kind of loads are connected. What is the update-rate of the control loop. He needs to do many design-iterations..
Everything I have said is just theory. Real world application is different. I would try to avoid complicated active filters.
That battery charger is a good example of a system you can easily measure, and then design a working filter.