Hi,
There is a Extract Single Tone Information.vi that is available from All Functions >> Analyze >> Waveform Measurements. This VI takes a time signal in and returns a detected phase (deg) out. Therefore, you can use one of these VIs for each sine wave and take that difference to determine the phase difference of your sine waves as a function of time.
Note that the Extract Single Tone Information.vi is not available LabVIEW Base package, but is available in all other LabVIEW packages.
Thanks again and have a great day!
Kileen C.
Applications Engineer
National Instruments