Although, all the techniques mentioned about has some merit on surface topography but according to study and number of query to be solved "AFM" stands out rightly first.
Reason behind this .....it can define surface morphology, topology, thickness as well as to much extent dimension of particles on the thin film or deposition.
It is still a very cumbersome techniques if we compare it with other but it benifits researchers in solving major query related with the surface.
It depends on the scale of the dimensional details. If you are looking at a nanosurface with topographic details AFM can be used. Micrometer level topographic details can be best viewed and imaged in an SEM.
There isn't "the best method". Every techniques are suitable for own tasks.
The question is very broad and it is impossible to answer shortly.
TEM is a powerful tool for ultrastructure examination of some samples with high (in some cases - atomic) resolution. A conventional TEM specimen is a metal grid (diameter 3 mm) with a support film (carbon, fomvar, etc.). The objects are deposited on this film - small particles or ultrathin slices. Obviously, TEM is useful for morphological study of nanostructures, but it is impossible to examine the surface of bulk samples by this method.
SEM provides the surface topography of bulk samples (e.g. it is possible to put a conventional brick to SEM) with very width band of magnifications - from 10x to 1000000x (FE-SEM with special preparation). It is very simple and useful technique for medium (1000x - 50000x) magnification, but high resolution claims serious sample preparation and high skills of an operator.
AFM provides the nanorelief of the surface with high resolution - vertical resolution can be subangstrom (!) and lateral resolution is limited by tip's sharpness (10-20 nm for conventional probes and
AFM is better for surface topography as it will provide you with 3D view of the surface. AFM is actually the surface mapping of the material while SEM and TEM are the images clicked. STM is also used for surface mapping but I dont know much about that technique. So if you just need surface topography then it is AFM and STM can also be used.