We present an integrated procedure for the synthesis of infinite-layer nickelates using molecular-beam epitaxy with gas-phase reduction by atomic hydrogen. We first discuss challenges in the growth and characterization of perovskite NdNiO3/SrTiO3, arising from post growth crack formation in stoichiometric films. We then detail a procedure for fully reducing NdNiO3 films to the infinite-layer phase, NdNiO2, using atomic hydrogen; the resulting films display excellent structural quality, smooth surfaces, and lower residual resistivities than films reduced by other methods. We utilize the in situ nature of this technique to investigate the role that SrTiO3 capping layers play in the reduction process, illustrating their importance in preventing the formation of secondary phases at the exposed nickelate surface. A comparative bulk- and surface-sensitive study indicates that the formation of a polycrystalline crust on the film surface serves to limit the reduction process.