My DS is a 3C. We live in the Poconos. We drove him to INDOC and he filed for reimbursement. For his other travels (1st sailing, drill teams) the Academy makes/pays the flight reservations. Ground transport is reimbursed.
He is generally required to fly out of LaGuardia, although since his 2nd sailing is MSC and the DoD is covering cost (instead of DoT), he can fly out of our local airport. Much more convenient since I-95, the George Washington and Throgs Neck are "unfun" especially during rush hour, accidents, bad weather, bridgegate, etc...
BH