Punta Cana-Santo Domingo route definitely has its roads in better shape. The PUJ route is mostly smooth driving with the exception of a small area coming out of Veron from the airport that may have a pothole here and there. The POP Airport to Navarette portion of the North-South route needs repairs, and getting out of POP is very time-consuming because of major repairs going on.
But if you get two extra days to enjoy, then it is a no brainer.
As Hillbilly says, depending on your arrival time, take the airport taxi to the Metro station in Puerto Plata Metro. Luggage loading is easy and the bus makes a stopover in Santiago. No problem with kids.
Caribe Tours is another option. They have a terminal in Sosua and Puerto Plata, but for waiting with kids, the Metro terminal in Puerto Plata is better, so make it your first choice.
These express buses leave from Puerto Plata to Santo Domingo from 6 am to 8:15 pm
Get there half an hour before bus departure, unless it is a peak travel time, such as a holiday. If you are traveling on Sunday, get there an hour earlier.
DR1 - Travel - Holidays 2007
Metro Bus (Tel. 809 586-6062) Calle Beller corner Calle 16 de Agosto has six departures from Puerto Plata. Departures are at 6, 7, 9, 11 am and 2, 4 and 6:30 pm. Tickets are RD$275.
Caribe Tours (Tel 809 576-0790). Buses from Puerto Plata at 6 am, 6:45, 7:15, 8:15, 9:15, 10:15, 11:15, 12:15 pm, 1:15, 2:15, 3:15, 4:15, 5:15, 6:15, 7:15, 8:15 pm.