起飛的時間 means the exact time of your flight, for example, my plane will take off at 3 pm 起飛的時候 means the moment, for example, when your plane takes off, you need to buckle up!

起飞的时间 is better. For instance 飞机起飞的时间是今天早上九点。 Also a shorter version 起飞时间 is very commonly used.