Wake vortices-strong, coherent air turbulences created by aircrafts-pose a significant risk to aviation safety and therefore require accurate and reliable detection methods. In this paper, we present an advanced, explainable machine learning method that utilizes Light Detection and Ranging (LiDAR) data for effective wake vortex detection. Our method leverages a dynamic graph CNN (DGCNN) with semantic segmentation to partition a 3D LiDAR point cloud into meaningful segments. Further refinement is achieved through clustering techniques. A novel feature of our research is the use of a perturbation-based explanation technique, which clarifies the model's decision-making processes for air traffic regulators and controllers, increasing transparency and building trust. Our experimental results, based on measured and simulated LiDAR scans compared against four baseline methods, underscore the effectiveness and reliability of our approach. This combination of semantic segmentation and clustering for real-time wake vortex tracking significantly advances aviation safety measures, ensuring that these are both effective and comprehensible.