For the purpose of creating single-molecule junctions, which can convert a temperature difference ΔT into a voltage ΔV via the Seebeck effect, it is of interest to screen molecules for their potential to deliver high values of the Seebeck coefficient S = −ΔV/ΔT. Here we demonstrate that insight into molecular-scale thermoelectricity can be obtained by examining the widths and extreme values of Seebeck histograms. Using a combination of experimental scanning-tunnelling-microscopy-based transport measurements and density-functional-theory-based transport calculations, we study the electrical conductance and Seebeck coefficient of three endohedral metallofullerenes (EMFs) Sc3N@C80, Sc3C2@C80, and Er3N@C80, which based on their structures, are selected to exhibit different degrees of charge inhomogeneity and geometrical disorder within a junction. We demonstrate that standard deviations in the Seebeck coefficient σS of EMF-based junctions are correlated with the geometric standard deviation σ and the charge inhomogeneity σq. We benchmark these molecules against C60 and demonstrate that both σq, σS are the largest for Sc3C2@C80, both are the smallest for C60 and for the other EMFs, they follow the order Sc3C2@C80 > Sc3N@C80 > Er3N@C80 > C60. A large value of σS is a sign that a molecule can exhibit a wide range of Seebeck coefficients, which means that if orientations corresponding to high values can be selected and controlled, then the molecule has the potential to exhibit high-performance thermoelectricity. For the EMFs studied here, large values of σS are associated with distributions of Seebeck coefficients containing both positive and negative signs, which reveals that all these EMFs are bi-thermoelectric materials.