In the past years halide capping became one of the most promising strategies to passivate the surface of colloidal quantum dots (CQD) in thin films to be used for electronic and optoelectronic device fabrication. This is due to the convenient processing, the strong n-type characteristics and ambient stability of the devices. Here we investigate the effect of three counterions (ammonium, methylammonium and tetrabutylammonium) in iodide salts used for treating CQD thin films, and shed light to the mechanism of the ligand exchange. We obtain two- and three-dimensional square-packed PbS CQD superlattices with epitaxial merging of nearest neighbor CQDs as a direct outcome of the ligand-exchange reaction, and show that the order in the layer can be controlled by the nature of the counterion. Furthermore, we demonstrate that the acidity of the environment plays an important role in the substitution of the carboxylates by iodide ions at the surface of lead-chalcogenide quantum dots. Tetrabutylammonium iodide shows lower reactivity compared to methylammonium- and ammonium iodide due to the non-acidity of the cation which eventually leads to higher order, but also poorer carrier transport due to incomplete removal of the pristine ligands in the QD thin film. Finally, we show that single-step blade-coating and immersion in a ligand exchange solution such as the one containing methylammonium iodide can be used to fabricate well performing bottom-gate/bottom-contact PbS CQD field effect transistors with record subthreshold swing.