Should I travel to shantou from Hong Kong or Guangzhou?

Actually, your final destination is Puning, right?
If so, I suggest you travel via Guangzhou, where you can have easier access to the transportation.

Both the train and the bus area available. Take the train from Guangzhou Eat Railway station to Puning, and the duration is about 100 mins.

Buses are available at Tianhe Bus Station and Provincial Bus Station.