Carbon fiber-reinforced polymer (CFRP) composites are extensively used in aerospace, automotive, and marine structures due to their high stiffness-to-weight ratio; however, their dynamic performance is highly sensitive to delamination damage and laminate configuration. Recent advances in nanotechnology indicate that carbon nanotube (CNT) reinforcement can significantly enhance matrix-dominated properties and improve damage tolerance. This study investigates the vibration behavior of delaminated CNT-reinforced CFRP composite plates by examining the combined effects of CNT content, delamination size, stacking sequence, and boundary conditions. Natural frequencies and mode shapes are predicted using finite element modeling in ANSYS and an analytical Rayleigh–Ritz formulation implemented in MATLAB. Experimental modal testing is also conducted to validate the numerical and analytical results. Cross-ply, angle-ply, and quasi-isotropic laminates with CNT weight fractions of 0%, 0.5%, and 1.0% are analyzed under simply supported, clamped–clamped, and free–free boundary conditions. The results demonstrate that CNT reinforcement significantly increases natural frequencies and mitigates stiffness degradation induced by delamination, with quasi-isotropic laminates showing the highest sensitivity to CNT enhancement. For all configurations, natural frequencies decrease monotonically with increasing delamination size, while clamped boundary conditions consistently yield the highest frequency values. Excellent agreement is observed among finite element, analytical, and experimental outcomes. These findings provide valuable insights for vibration-based design and damage-tolerant optimization of CNT-enhanced composite structures in advanced engineering applications.