The nvtt library supports compression and generation of cube maps.
The nvcompress command line tool does not allow you to provide separate images for each of the cube map faces, but allows you to provide cube maps as DDS files.
The nvassemble command line tool allows you to assemble a cube map from different images, so you can generate a cube map in two steps. First assemble it with nvassemble, that produces a DDS file that you can then compress with nvcompress.
The nvcompress command line tool does not allow you to provide separate images for each of the cube map faces, but allows you to provide cube maps as DDS files.
The nvassemble command line tool allows you to assemble a cube map from different images, so you can generate a cube map in two steps. First assemble it with nvassemble, that produces a DDS file that you can then compress with nvcompress.