You could head to the train stations first and then take a high speed train to Nanjing which takes only 1.5hrs. Shanghai Hongqiao station and Shanghai station all have trains departing to Nanjing, but they are located in different districts. Shanghai train station is located in Zhabei District while Hongqiao station is situated close to Hongqiao Airport. From Pudong airport, you can take the airport bus line 5 to Shanghai train station or subway line 2 to Hongqiao station.