DC-DC Converter: Periodic Ripple
It looks like you have chosen not the best part for the job. 

First, the converter is UNREGULATED, so you will have substantial output variability when load changes. It may or may not be important however. 

Second, you definitely have no use of SYNCOUT signal. From the block diagram it looks like its amplitude is huge, and there will be very difficult to avoid EMI. Even if you will use heavy L-C filters on power rails (since the ripple level is 50mV by specs), it will be difficult to shield the susceptible electronics from over-the air EMI.

I am afraid you need either to make another selection, or shield the entire DCDC on all sides, with all care for ground layout. In any case you will likely need to spin the PCB.