Active LPF with cut-off frequency ~4250 Hz lets a 20 KHz signal through
Back of the envelope calculation...
20k/4250 = about 4
It's a second order filter, so at a frequency 4x above its -3dB point it should attenuate the signal by 4 squared, or about 16.
Output signal is about 0.3Vpp.
Input signal is 5Vpp.
5/0.3 = about 16.
So it delivers the correct attenuation.
If you want more attenuation, use a lower -3dB point, or a higher order filter, or a much higher PWM frequency so it gets attenuated a lot more.
If you used a high -3dB point of 4250 Hz because you wanted fast settling time, then don't use a PWM for analog output when you want fast settling time, unless your micro supports high PWM frequencies. Use a DAC instead.

if the op amp is switched for different models such as LT1001, the output voltage level is around a few pV.

Did you forget the opamp power supplies?