This study evaluates the performance of LiDAR sensing and UAV photogrammetry for three-dimensional canopy reconstruction and structural parameter estimation in precision agriculture. Experiments were conducted in Sicily (Italy) on Moringa oleifera Lam. and Ficus macrophylla subsp. columnaris, representing contrasting canopy architectures. LiDAR and UAV data were used to generate canopy models and estimate canopy height, volume, and vegetation density. A voxel-based approach was applied to LiDAR point clouds to analyze internal canopy structure. LiDAR significantly outperformed UAV photogrammetry, achieving lower errors in canopy height estimation (RMSE = 0.19–0.21 m vs. 0.52–0.60 m) and canopy volume (3.5–4.2% vs. 13.7–16.1%). UAV photogrammetry provided reliable estimates of canopy surface but underestimated structural parameters in dense vegetation due to occlusion effects. Differences were more pronounced in Ficus macrophylla than in Moringa oleifera, highlighting the influence of canopy complexity. These findings demonstrate that LiDAR-derived structural metrics can improve canopy characterization and support precision agriculture applications such as biomass estimation, irrigation planning, and canopy management in Mediterranean cropping systems.