If you take a look at the NI Examples there is one named
Counter - Read Pulse Width and Frequency (Continuous).vi
Browse according to Directery Structure and look at
DAQmx>>>Counter Input>>>Counter - Read Pulse Width and Frequency (Continuous).vi
In that VI, there is a tab for 2 Edge Separation measurement. If you run the VI with this tab selected it will give you the time between edges of the two waveforms. You wil lthen have to convert the time to a phase (based on the frequency of the two waveforms). I ran it with ctr0 selected and first and second inputs were PFI8 and PFI9.
If you open up this example from NI Example Finder, you'll see a section called "Requirements" in the bottom right corner of the window. This lists the DAQ hardware compatible with the highlighted example.