Hey mtgregor!
It really depends on both how fast the frequency we are looking at is, as well as how synched up you need these signals to be. Obviously, it takes some period of time for a frequency measurement to occur. This is because the VI will count the number of edges on the counter over some period of time and use that to determine the frequency, whereas the analog input is a value at a specific point in time.
If you are looking for software synchronization in the range of milliseconds your synchronization can be accomplished just through dataflow programming, ie. by placing your frequency VI in the while loop to run parallel to the read VI.
If you are looking for a more hardware timed solution, you are going to need to count digital edges on your pulse. There is a good example that shows this in the DAQ examples in the LabVIEW's example finder, called Count Buffered Edges.