X-ray structural analysis, together with steady-state and transient optical spectroscopy, is used for studying the morphology and optical properties of quantum dot superlattices (QDSLs) formed on glass substrates by the self-organization of PbS quantum dots with a variety of surface ligands. The diameter of the PbS QDs varies from 2.8 to 8.9 nm. The QDSLs period is proportional to the dot diameter, increasing slightly with dot size due to the increase in ligand layer thickness. Removal of the ligands has a number of effects on the morphology of QDSLs formed from the dots of different sizes: for small QDs the reduction in the amount of ligands obstructs the self-organization process, impairing the ordering of the QDSLs, while for large QDs the ordering of the superlattice structure is improved, with an interdot distance as low as 0.4 nm allowing rapid charge carrier transport through the QDSLs. QDSL formation does not induce significant changes to the absorption and photoluminescence spectra of the QDs. However, the luminescence decay time is reduced dramatically, due to the appearance of nonradiative relaxation channels.