Flying quadrotors in tight formations is a challenging problem. It is known that in the near-field airflow of a quadrotor, the aerodynamic effects induced by the propellers are complex and difficult to characterize. Although machine learning tools can potentially be used to derive models that capture these effects, these data-driven approaches can be sample inefficient and the resulting models often do not generalize as well as their first-principles counterparts. In this work, we propose a framework that combines the benefits of first-principles modeling and data-driven approaches to construct an accurate and sample efficient representation of the complex aerodynamic effects resulting from quadrotors flying in formation. The data-driven component within our model is lightweight, making it amenable for optimization-based control design. Through simulations and physical experiments, we show that incorporating the model into a novel learning-based nonlinear model predictive control (MPC) framework results in substantial performance improvements in terms of trajectory tracking and disturbance rejection. In particular, our framework significantly outperforms nominal MPC in physical experiments, achieving a 40.1% improvement in the average trajectory tracking errors and a 57.5% reduction in the maximum vertical separation errors. Our framework also achieves exceptional sample efficiency, using only a total of 46 seconds of flight data for training across both simulations and physical experiments. Furthermore, with our proposed framework, the quadrotors achieve an exceptionally tight formation, flying with an average separation of less than 1.5 body lengths throughout the flight. A video illustrating our framework and physical experiments is given here: https://youtu.be/Hv-0JiVoJGo