What's wrong with the dxtex tool? (Ok, other than a mediocre UI)
You could create the cube map at runtime by drawing the 6 faces into a new cube map
http://msdn.microsoft.com/en-us/library/microsoft.xna.framework.graphics.rendertargetcube.aspx
ATI AMD has CubeMapGen, which a a bunch more options and lets you save a DDS file.
http://developer.amd.com/gpu/cubemapgen/pages/default.aspx
You could probably also make your own content processor to stitch them together.