Ferrite beads come in various types designed for the specific uses. Your observation indicates that those you selected resonate with the 100 capacitor and generate the ripple you observed.
A good advice is difficult. I would order several bead types and test them over the frequency range of interest. If they fail, simply use only the capacitor if the results are good.
Ripple can also be reduced by a RC in series, e.g. 5-10 Ohms in series with a 0.1 to 10 uF capacitor.
Apparently, similar situation happens with many DC-DC converters on the market I observed such ripple on some I needed to use, and the RC combination as above served me well.
To power sensitive circuits like microwave PLOs, I recommend to use "linear" voltage regulators and rectifiers. The ripple is often difficult to reject.