This paper describes a hierarchical solution consisting of a multi-phase planner and a low-level safe controller to jointly solve the safe navigation problem in crowded, dynamic, and uncertain environments. The planner employs dynamic gap analysis and trajectory optimization to achieve collision avoidance with respect to the predicted trajectories of dynamic agents within the sensing and planning horizon and with robustness to agent uncertainty. To address uncertainty over the planning horizon and real-time safety, a fast reactive safe set algorithm (SSA) is adopted, which monitors and modifies the unsafe control during trajectory tracking. Compared to other existing methods, our approach offers theoretical guarantees of safety and achieves collision-free navigation with higher probability in uncertain environments, as demonstrated in scenarios with 20 and 50 dynamic agents. Project website: https://hychen-naza.github.io/projects/HDAGap/.