As I know, there is no direct bus from Pudong Airport to Nanjing currently. So, when you exit from the baggage claim area, please follows the signs which could guide you to the shuttle bus station, both in T1 and T2. Then, please catch the bus Line 5, the terminal of which is Shanghai Railway Station. This line is in operation from 07:00 to 23:00, and takes 222RMB.

At the railway station, you could take an express train to arrive in Nanjing in 3 hours. Well, you could search the train infor in details at https://www.travelchinaguide.com/china-trains/