I recommend adding a PI filter, Just add another LC filter after the voltage regulators output to smooth out the voltage fluxuations. I would also recommend using a TL431 adjustable zener diode instead of using a resistor voltage divider, since it will provide a much stabilier reference voltage. Your reference voltage is suspitable to the Vdd noise. A second TL431 in the voltage feed back divider will also add to stability of the feedback loop. Using a small 100 pf to 10 nf cap across r5 would also increase feed back stablity. A small cap will smooth out some of the switching noise and help prevent the Op-amp from over-compensating the switching noise that tends to cause a feedback amplication of the switching noise. For output loads with fast current demand changes a bigger cap will be need to keep the feedback circuit stable.
Google for "TL431 voltage regulator feedback" for example designs. You also need a decouping cap across the the op-amps voltage supply since the 5V input noise will impact the output of the op-amp.
FWIW: adding the external op-amp is likely making the problem worse, especially if your powering the op-amp from the regulator output. The regulator built in circuitry will likely provide a more stable, and lower noise output then you will achieve using an external Op-amp feedback controller.
Choosing the right switching inductor also makes a big difference. The low value induction you choose will provide lower noise when the output load is near the middle of the PWM duty cycle. At low output current it will create more noise. If your application has a low current demand choose a higher inductor value. Also the input voltage is a factor in the inductor size. If your using a high input voltage you want to use a higher inductor value. if the input voltage is low than you want to use a lower inductor value. With a small inductor and a high input current, the PWM duty cycle will drop very low. This makes it difficult for the regulator circuity to accurately turn on and off the the switching transistor. Try connecting a probe to the input side of the inductor and monitor the duty cycle. If it's very small, than try adding a bigger value inductor.
For low output noise with a Buck regulator an LC filter is a must. Add a second inductor and cap after the output to dramatically reduce your output noise. If you need a low\zero ripple output than try adding a coupled inductor as your output inductor:
http://www.hamill.co.uk/pdfs/ciabfbb_.pdf (Coupled inductor filters)
A coupled inductor is a inductor with a bifilar pair winding. One Winding is connected between source and output. The other between source a low esr cap and ground. The second winding absorbs the AC noise (ripple) and diverts it to ground.