This work focuses on channel estimation in extremely large aperture array (ELAA) systems, where near-field propagation and spatial non-stationarity introduce complexities that hinder the effectiveness of traditional estimation techniques. A physics-based hybrid channel model is developed, incorporating non-binary visibility region (VR) masks to simulate diffraction-induced power variations across the antenna array. To address the estimation challenges posed by these channel conditions, a novel algorithm is proposed: Visibility-Region-HMM-Aided Polar-Domain Simultaneous Orthogonal Matching Pursuit (VR-HMM-P-SOMP). The method extends a greedy sparse recovery framework by integrating VR estimation through a hidden Markov model (HMM), using a novel emission formulation and Viterbi decoding. This allows the algorithm to adaptively mask steering vectors and account for spatial non-stationarity at the antenna level. Simulation results demonstrate that the proposed method enhances estimation accuracy compared to existing techniques, particularly in low-SNR and sparse scenarios, while maintaining a low computational complexity. The algorithm presents robustness across a range of design parameters and channel conditions, offering a practical solution for ELAA systems.