Don't forget that thunder is the noise you hear when lightning causes the rapid expansion of the air. Lightning can occur within clouds or from cloud to cloud, and may not be visible to you. Better people than me will confirm or deny whether aircraft can trigger lightning, but I think they can as they can present the electric imbalance (+ve to -ve) that the lightning needs to trigger. If it did so, I imagine the aircraft would suffer or report a lightning strike.
Another explanation might be that you heard the reverberation of the engine noise within or between the clouds and/or the ground.
Short answer: don't know!!
