The sea is the same Caribbean Sea. The beach will depend on your hotel. There are only very slight differences in the beach strips in front of each hotel.
To help you make up your mind, see:
http://dr1.com/travel/puntacana/
http://dr1.com/travel/laromana/
You will probably be making it back into Santo Domingo to go to Samana. If that is the case, then you will be closer by staying in La Romana (it's two more hours to Samana). You should plan on overnighting in Santo Domingo to see the Colonial City. Then take the Metro Bus to Samana. It's a four hour trip from Santo Domingo to Samana.