It takes 1 hour by bus from Nanjing Station to the airport, and Zhonghua Gate is much closer to the airport than Nanjing Station.
It takes about ten minutes from Nanjing South Railway Station to Zhonghuamen Station.
Consider getting out of the South Station and then entering the South Subway Station. It's almost a quarter of an hour.
Even if the bus 1 hour, it will arrive at Lukou airport before four o'clock.
Unless it's an international flight, it should be enough ~