First of all, what is the frequency that you are trying to measure with this method? As you mentioned you need a sampling rate that is much faster than the frequency you are trying to measure. Nyquist says you have to go at least two times, but the more samples you get the more accurate the "Extract Single Tone measurement" will be. Keep in mind that the AI 100 max update rate is about 360Hz. Also, you will have to get the samples into an array and pass it to the VI. The more periods of the wave you pass the more accurate it will be as well. Lastly, if you are not getting good results you should try to convert the frequency analog wave to a square wave of the same frequency. Doing this will allow you to use one of the counter modules for Fieldpoint, which can measure frequencies much higher using counter techniques.
I hope this information helps,
Rick Kuhlman