FreqCounter for very low frequencies (below 100 Hz or something) isn't the best thing you can do to count cycles.
As someone told you, you would need to measure the length of the pulse instead (FreqMeasure, FreqPeriod, InputCapture, pulseIn, millis()/micros() ).
Since at dark time it's rare to get more than 10,000Hz with those sensors, I think FreqCounter isn't useful at all for this project.