First, Dr. Aday says you should get up once every hour when in the air, which means it would be helpful to book the aisle seat. While seated, Aday suggests doing little stretches like flexing and relaxing your calf muscles, rolling ankles, and clenching and spreading toes. This will all help to get the blood flowing.
There are also a ton of pre-boarding stretches you can do to prevent soreness after a flight. For instance, Men's Health recommends doing a stretch that affects your hip flexors and quads at the gate. Also, Women's Health outlines a few stretches to be done pre-boarding, suggesting a standing calf stretch and a kneeling hip flex among others. Finally, these airport yoga poses will keep you calm and loose.