How would I test if my low pass filter works on a remote FPGA?
The easiest for you is to drive the filter digitally. You will need some form of storage for the filter's input signal, and for the filter's output signal.
Suitable storage are embedded ROM, Register Files (2D bank of flops), or embedded RAM. You read the signal sample-by-sample from storage, apply it to the filter, and write the output sample-by-sample into storage. Then you need to dump the output for inspection, or apply further logic to compare it to a reference vector that you also stored.
You should also look at Altera's signaltap (for Xilinx there's chipscope), which allow you to capture and plot FPGA's internal signals. These may significantly simplify the task of applying a test vector and viewing the result.
If you want to use analog signals you will need to have a board with ADC and 2 DACs. You can use one DAC to generate an analog signal and feed it back into the FPGA via the ADC, then filter it and output it from the DAC to hear the audio or view the analog signal on a scope.