Ferrite bead vs common mode choke
It depends on the environment of your board. Let's call the negative pole of your supply voltage GND. For example in a car, the whole chassis is GND, but you are connected only at your supply pins, not directly on the chassis. 
Your board has an parasitic capacitance against chassis, so noisy HF current will flow there. If you have a case like this, the common mode choke will help, because the HF current will need through your VCC and your GND supply line. 

If your board creates some kind of other HF-Noise internal, a switching regulator, or some kind of CPU or memory interface, most of the current flows from the high-speed signal to your internal GND (High speed switching). The commom mode choke won't prevent the noise from getting out of your design, because there is a current flowing in and a current flowing out the same time. In this case a Ferrite Bead would be an better choice.

I suggest you to keep the ferrites for some reasons.
Common Mode problems can be eliminated, if your signals on the board have an greater capacitance to your internal GND as against the chassis or some other external devices. In addition to that, ferrites are cheaper most time. 
I don't know your specification, however, i work in automotive industry, i would take the ferrites.