Process the data in the frequency domain as real/imaginary components as opposed to amplitude/phase. It is hard to work with phase information, but doing signal processing on the real/imaginary components isn't too bad.
Most of the variations in the phase are usually at locations where the amplitude is low and so the noise at that frequency is of the same order of magnitude. If your signal of interest is located at these frequencies and of such low amplitude, you have more of a problem than filtering will fix. Either oversampling or ensemble averaging will be required to reduce the noise.
If there is sufficient signal present at the frequencies of interest, then the phase at those frequencies should be pretty stable.
Randall Pursley