(Audio) Line Level RC - 24db LPF
I reckon the huge output capacitance of your filter is not ideal. If 16.8 dB attenuation per decade still fulfills your requirements, you could use the following circuit:

You were also burning a lot of current through your BJT. I have increased the collector's resistance and the base bias resistor.
If you still need a higher gain, say 40dB decade, you can use a second order low pass like the Sallen-Key filter described here.