It's a long drive from Santiago to Bayahibe (sorry not sure of exact times but I think around 2hours to central Santo Domingo and a further 2 hours to Bayahibe).
Most excursion boats leave Bayahibe around 10am and return to Bayahibe between 4.30pm and 5pm. That means an early start and leaves you with a drive back to Santiago in the dark.
You could always stay overnight in a cheap hotel like Hotel Bayahibe.
There are many Saona excursion companies out there. Some use a combo of speed boat out (40 minutes to Saona) and catamaran back (2hours using mix of motor and sail). Some only use speed boats (20-25 person lanchas - fast and bumpy ride).
Some tours are booze cruise, party boats (70 person capacity), some focus on the eco side for smaller groups visiting the less crowded beaches (google Seavis, Pro Excursions and Bayahibe Fishing Centre).
Bayahibe also has taxi boats run by ASPLABA. You hire these for private groups, price depends on number in group and your negotiation skills. Saona is part of the National Park of the East so you need to buy $US3 wrist bands from the admin office in the main bus car park. Most organised excursions will include this in the price.
All tours will stop on the way there or back at the Piscina Natural, a shallow, off shore area with crystal clear water and starfish.
The nicest and less crowded beaches are on the south east side - Canto de la Playa and Pepe's beach.
Best snorkeling is at Cayo Raton on the north east side near Catalinita island (Seavis go there). Depending on the water conditions you can also snorkel at the remains of the old pier on Catuano beach.
The big catamarans can not enter the mangrove area.
There's a turtle sanctuary in Saona village Manu Juan.
Have fun!