Two dimensional (2D) transition-metal dichalcogenide (TMD) based semiconductors have generated intense recent interest due to their novel optical and electronic properties, and potential for applications. In this work, we characterize the atomic and electronic nature of intrinsic point defects found in single crystals of these materials synthesized by two different methods - chemical vapor transport and self-flux growth. Using a combination of scanning tunneling microscopy (STM) and scanning transmission electron microscopy (STEM), we show that the two major intrinsic defects in these materials are metal vacancies and chalcogen antisites. We show that by control of the synthetic conditions, we can reduce the defect concentration from above 1013 /cm2 to below 1011 /cm2. Because these point defects act as centers for non-radiative recombination of excitons, this improvement in material quality leads to a hundred-fold increase in the radiative recombination efficiency.