Two new complexes, [Co(N3L)2](NO3)2·6H2O (complex 1) and [Ni(N3L)2](NO3)2·6H2O (complex 2), have been synthesized using the organic heterocyclic chelating ligand N3L [4-(1-methylimidazole)-2,6-di(pyrazinyl)pyridine] and characterized primarily by single-crystal X-ray diffraction. In addition to detailing the crystal structures of these complexes, we highlight their distorted octahedral geometries and diverse supramolecular interactions, including π···π stacking, anion···π interactions, and hydrogen bonding. These interactions play a crucial role in shaping the distinct 1D, 2D, and 3D supramolecular architectures of both complexes. Notably, noncoordinated water molecules assemble into hexameric water clusters (H2O)6, which are key stabilizing factors for the 3D structures in the solid state. To gain deeper insight into these noncovalent interactions, we performed density functional theory (DFT) calculations combined with quantum theory of atoms in molecules (QTAIM) and noncovalent interaction plot (NCIplot) analyses. These studies allowed us to explore the nature of anion···π interactions and hydrogen bonding within the water clusters. Additionally, the electronic properties of the complexes were investigated through electrical characterization of as-fabricated Schottky diodes, revealing their potential applications in Schottky-diode-based electronic devices. Notably, in the Schottky device structure, complex 1 demonstrated superior electrical transport properties compared to complex 2 followed by its lower bandgap, better conductivity, and lower Schottky barrier height. Furthermore, we analyzed the optical properties of the Co complex (complex 1) as a model system using band structure analysis, density of states (DOS), and projected density of states (PDOS) calculations. The superior performance of complex 1 has also been explained with proper theoretical justification.