Hi "Big" Jim,
That's a very complex question to answer as you're essentially comparing the speed of running FFT + the max measurement on the scope + transferring the result of that measurement to your PC versus the speed of transferring the waveform to the PC and doing the FFT + measurement there.
My guess is that running the FFT and max measurement on the scope and then transferring just the result of max would be significantly faster than the other option, but I don't know the speed of your connection or computer.
If you have the time to test both, that would be ideal.