Without reading very carefully all the proposed solutions, the OP problem looks to me like an ideal application for a lock-in amplifier, simply because there is prior knowledge of the Tx signal.
There were some quadrature based solutions mentioned, not sure if those will eventually implement an ad-hoc lock-in amplifier or not (at a draft look I perceived them as an implementation of a heterodyne).
I'll go for the homodyne method first (in EE also known as a lock-in amplifier, in optics known as an interferometer) and see if it can get the required resolution. Also very important, try to make use of all of the prior knowledge, including expected S/N, expected frequency shift ranges, rate of frequency change.
I never had to solve a similar problem, so my advice might be completely off.
Whatever method you'll choose, "One can not find what one is not looking for", here meaning if you want to squeeze out the best results out of those few samples, you
must take advantage of any prior knowledge you have about them, here the most important is that you
have the original Tx-ed signal, followed by the expectations about the Rx signal (expected S/N, deviation range, etc.).
Chances are you might be able to
vary the Tx signal parameters, too (from the OP is not very clear if this is allowed). If true, this ability might improve the end results even more, depending on the exact application (e.g. the chirp modulation in radar/sonar type of applications).