The AFNI GUI can show you the xyz coordinates in RAI or LPI order or IJK indices for the storage order. If the datasets are aligned then the xyz coordinates are equal. To get the datasets to match, use align_epi_anat.py or one of the align options in afni_proc.py. You can move the crosshairs in the image viewer by right-clicking on the image and jumping to an xyz position or an ijk position. The Define Datamode, Misc menu allows showing ijk indices instead of xyz coordinates.

If you would like to find the center of the voxel from one dataset that corresponds to the center of a voxel from another dataset, you can use the AFNI GUI. The centers are slightly different between the two datasets because of differences in the sampling grid positions and resolution. This is easiest to see with two controllers open and your func and anat datasets open as the underlay in each. The crosshairs coordinates are reported in the upper left of each controller's menu. One could also switch the background image by toggling between the underlay and the overlay dataset by typing the letter 'u' on the image viewer window.

If you would like the coordinates of the corresponding voxel to be reported on the command line or in a script, something would need to be written. It shouldn't be difficult, I think, but let us know.