USB 5v power filtering
Could you specify more information, such as load conditions per port, source port info, etc? 

One way you might solve this is to use LTSpice or similar simulator to play around with various loads and filtering capabilities.

LC filters can be effective, but the current can require a very large inductor. The larger the inductor, the smoother the current ripple. You may consider adding a TVS shunt for any spikes.