Two-dimensional (2D) materials and heterostructures are promising candidates for nanoelectronics. However, the quality of material interfaces often limits the performance of electronic devices made from atomically thick 2D materials and heterostructures. Atomic force microscopy (AFM) tip-based cleaning is a reliable technique to remove interface contaminants and flatten heterostructures. Here, we demonstrate AFM tip-based cleaning applied to hBN-encapsulated monolayer MoS2 transistors, which results in electrical performance improvements of the devices. To investigate the impact of cleaning on device performance, we compared the characteristics of as-transferred heterostructures and transistors before and after tip-based cleaning using photoluminescence (PL) and electronic measurements. The PL linewidth of monolayer MoS2 decreased from 84 meV before cleaning to 71 meV after cleaning. The extrinsic mobility of monolayer MoS2 field-effect transistors increased from 21 cm2/Vs before cleaning to 38 cm2/Vs after cleaning. Using the results from AFM topography, photoluminescence, and back-gated field-effect measurements, we infer that tip-based cleaning enhances the mobility of hBN-encapsulated monolayer MoS2 by reducing interface disorder. Finally, we fabricate a MoS2 field-effect transistor (FET) from a tip-cleaned heterostructure and achieved a device mobility of 73 cm2/Vs. The results of this work could be used to improve the electrical performance of heterostructure devices and other types of mechanically assembled van der Waals heterostructures.