<p>Metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) are two prominent classes of porous materials with exceptional properties for applications in gas storage, catalysis, and drug delivery, owing to their high surface areas and tunable structures. This study presents a computational analysis of these frameworks using degree-based and neighborhood degree based topological indices. We compute a comprehensive set of indices including Sombor variants, Zagreb indices, and NDe indices for two distinct structures: a 2D naphthalene-based MOF and a thiophene-based covalent triazine framework (COF). The behavior of these indices is graphically analyzed through 3D visualizations. Crucially, we validate the chemical relevance of these indices by developing quantitative structure-property relationship (QSPR) models for a series of phenethylamine derivatives. Our models demonstrate strong statistical correlations between the topological indices and key physicochemical properties, particularly molar volume, boiling point, and enthalpy of vaporization. This validation confirms the utility of topological indices as robust predictive tools for screening and optimizing MOF/COF materials, directly linking their molecular graph topology to performance-critical properties.</p>