Ionospheric scintillation causes major impairments to Global Navigation Satellite System (GNSS) in low-latitude regions. In severe scenarios, this event can lead to complete loss of lock, thus making GNSS measurements unusable for navigation. In this paper, we derive a cooperative localization algorithm where a set of partially connected aircraft exchange messages with neighboring nodes on the network to improve their own position estimates. We consider the scintillation events as abrupt changes in the measurement variance, which are modeled by a discrete-valued Markov process at the nodes which have access to GNSS measurements. Simulation results show that Markovian modeling and cooperation via factor graph message passing reduce the average 3D root mean square localization error and yield an average vertical position error that meets civil aviation standards for approach and landing.