Engineering nano-mechanical quantum systems possessing ultra-long motional coherence times allow for applications in ultra-sensitive quantum sensing, motional quantum memories and motional interfaces between other carriers of quantum information such as photons, quantum dots and superconducting systems. To achieve ultra-high motional Q one must work hard to remove all forms of motional noise and heating. We examine a magneto-nanomechanical quantum system that consists of a 3D arrangement of miniature superconducting loops which is stably levitated in a static inhomogenous magnetic field. The resulting motional Q is limited by the tiny decay of the supercurrent in the loops and may reach up to Q~10^(10). We examine the classical and quantum dynamics of the levitating superconducting system and prove that it is stably trapped and can achieve motional oscillation frequencies of several tens of MHz. By inductively coupling this levitating object to a nearby flux qubit we further show that by driving the qubit one can cool the motion of the levitated object and in the case of resonance, this can cool the vertical motion of the object close to its ground state.