Wind and turbulence, including wakes induced by leading aircraft, have a large impact on flight performance and flight safety of both manned and unmanned aircraft. An accurate real-time wind estimation technique is crucial for tasks such as increasing air traffic capacity, commercial formation flight, or aerial refueling, etc. A leader-follower formation flight of Phastball Unmanned Aerial Vehicles (UAVs) were used as the experimental platform for the above problem. The air data system of Phastball UAV was developed with pitot-tube and flow-angle sensors. Using the designed system, two Unscented Kalman Filters (one standalone UKF and one cooperative UKF) were developed for the wind field estimation with and without using the wake information from the leader aircraft. For close formation flights, the wake of the leader is assumed to be predictable by certain wake models for the follower aircraft. Flight data showed the effectiveness of the standalone EKF for the wind estimation compared with the ground weather station measurements. Simulation results showed the advantage of the cooperative UKF over the standalone UKF.