Harry,
the Guagua-routes from Puerto Plata and Nagua terminate in Rio San Juan at the road that goes into town (Caribe tours terminal is also next to it). Walk down this road to the other end (about 1/2 mile), there you find the boats, very easy.
I am not sure about the actual prices, but they became very expensive during the last years. I think in 1996 it was RD$300/boat, now it is RD$600.
My recommendation: Try to be there on a day with calm water. Do not go on a day with high waves, especially if the boaters tell you that they can not go to the open water. In that case they will offer you a "short" tour through the mangroves at maybe half the price, but it is only worth 1/4 of it.
"Make friends": The price is for up to 10 people in one boat. Try to find other tourists who share it with you, if you are there in the morning try to join a group from one of the tour busses. Boats can carry easily 20 people.
But I really recommend to take the tour, it is a highlight.
In the vicinity you find some nice bars and restaurants. Or even better: Go bathing and eat grilled fish at Playa Caleton, 1 mile east of Rio San Juan. To me the best beach all around.
BTW: Here you find some pictures:
http://www.playagrande.de/Bildatlas/Picture_Gallery/picture_gallery.html
Bye
Tibu