Best window before FFT ? (for a signal consisting of 2 tones used for phase measurement)
Using an FFT to measure phase for just two tones results in a lot more processing that doing the following alternate approach that can be either streamed or processed in blocks. No windowing is needed:
Apply the received signal as the input to two multipliers. Apply a normalized local copy of one tone as the second input to one of the multipliers and a normalized local copy of the other tone to the other. The low pass filter of each output will be an estimate of the phase given by$A\cos(\theta)$.
For full 360 degree phase resolution, use a complex local tone and two complex multipliers with two outputs (I, Q) with the phase determined using atan2(Q, I).   (This is essentially the operation in two bins of the DFT).