Trajectory prediction of aerial vehicles is a key requirement in applications ranging from missile guidance to UAV collision avoidance. While most prediction methods assume deterministic target motion, real-world targets often exhibit stochastic behaviors such as evasive maneuvers or random gliding patterns. This paper introduces a probabilistic framework based on Conditional Normalizing Flows (CNFs) to model and predict such stochastic dynamics directly from trajectory data. The learned model generates probability distributions of future target positions conditioned on initial states and dynamic parameters, enabling efficient sampling and exact density evaluation. To provide deterministic surrogates compatible with existing guidance and planning algorithms, sampled trajectories are clustered using a time series k-means approach, yielding a set of representative "virtual target" trajectories. The method is target-agnostic, computationally efficient, and requires only trajectory data for training, making it suitable as a drop-in replacement for deterministic predictors. Simulated scenarios with maneuvering and ballistic targets demonstrate that the proposed approach bridges the gap between deterministic assumptions and stochastic reality, advancing guidance and control algorithms for autonomous vehicles.