LC design for DC converters
You need to have two capacitors - one on either side of the inductor. The capacitor closest to the DC/DC input is an integral part of the switching converter circuit, and its performance must be carefully managed to ensure the DC/DC works properly. The capacitor on the other side of the inductor forms the second element of the LC input filter circuit that prevents conducted emissions from coming out of the DC/DC input into the supply lines.

Also note that design of the filter is not straight forward. An LC circuit can have a very high output impedance at the resonant frequency. This can create instability at the input to the DC/DC converter potentially making the noise worse, causing the regulator to become unstable, or even causing the input to exceed the maximum safe voltage level. You probably need to damp the input filter. There is a lot of useful information here:

http://www.ti.com/lit/an/snva538/snva538.pdf