Remote sensing technology is a timely and cost-efficient method for leaf area index (LAI) estimation, especially for less accessible areas such as mangrove forests. Confounded by the poor penetrability of optical images, most previous studies focused on estimating the LAI of the main canopy, ignoring the understory. This study investigated the capability of multispectral Sentinel-2 (S2) imagery, airborne hyperspectral imagery (HSI), and airborne LiDAR data for overstory (OLe) and understory (ULe) LAI estimation of a multi-layered mangrove stand in Mai Po, Hong Kong, China. LiDAR data were employed to stratify the overstory and understory. Vegetation indices (VIs) and LiDAR metrics were generated as predictors to build regression models against the OLe and ULe with multiple parametric and non-parametric methods. The OLe model fitting results were typically better than ULe because of the dominant contribution of the overstory to the remotely sensed signal. A single red-edge VI derived from HSI data delivered the lowest RMSE of 0.12 and the highest R2adj of 0.79 for OLe model fitting. The synergetic use of LiDAR metrics and S2 VIs performed best for ULe model fitting with RMSE = 0.33, R2adj = 0.84. OLe estimation benefited from the high spatial and spectral resolution HSI that was found less confounded by the understory. In addition to their penetration attributes, LiDAR data could separately describe the upper and lower canopy, which reduced the noise from other components, thereby improving the ULe estimation.