Is the frequency of the sinusoidal output proportional to the flow rate? If so, then you've got a variety of options:
1. If you're using a general-purpose data acquisition board, then you can use an analog input channel and a while loop to repeatedly read in N points of the sinusoid and do an FFT to determine the frequency and instantaneous flow rate.
2. For higher channel counts, there is special-purpose signal conditioning hardware such as the SCXI-1126 on the NI Web site that does the analysis in hardware.
Best Regards,
John Lum
National Instruments