Agree with moondog, if you are coming internationally and want to get to Nanjing with expediency, it would better to fly there. You may wish to consider flights coming from other Asian hubs that fly directly to NKG without first going through another Chinese gateway: MU and OZ nonstop flights ICN-NKG comes to mind, or MU, KA/CX, or HX via HKG. Not sure if there is anything nonstop from NRT or HND.

Of the cities you already outlined, SHA is the best approach to get to Nanjing by rail transfer. If there are no nonstops that work for you into NKG directly, then trying for a regional international route that goes to SHA (there are quite a few from HND, GMP, HKG, TSA) might work as a fallback.

Additional air-train data point:
From PEK. the switch to get to Beijing South Rail Station which is on the opposite side of town is not straightforward if you go by non-taxi method. Options are to take Airport Shuttle Bus (RMB 16) to Xidan, then switch to Subway line 4 southbound to BJ South. Or Airport Express Light rail to Dongzhimen hub to subway Line 2 to Line 1 to Line 4 (seriously NOT recommended.) Overall: not a good plan if you are trying to do a direct switch without a stayover in Beijing. If arriving in PEK and then connecting to a NKG domestic flight (make sure enough time!), that would be more logical.