The honest truth is that it depends - on the material, the complexity of the part, and the economic factors at play. 3D printing technology like FDM machines build parts from the bottom-up. They can create complex shapes and internal components somewhat more easily than a CNC machine. By contrast, conventional CNC machines are somewhat limited by the tools available and the axes of rotation the machine is capable of utilizing. On the flip side, FDM prototyping is much more limited by materials than is a machined block of material. For example, if you need a prototype of a living hinge you would want to use CNC and polypropylene. Want to learn more? Read here. Just about anything can be machined while by contrast only certain materials have been adapted into filaments suitable for 3D printing. 

Application For Manufacturing: Many novel CNC specialty machines are built specifically for niche manufacturing processes. For example, electrochemical machining is used to cut highly durable metal products not otherwise feasible. Conventional CNC machines are more adept at and typically used for prototype development than manufacturing.