Actually the ferry is travelling some days to Mayaguez and some days to San Juan.
On this page (is in spanish) says that they depart from Santo Domingo on Sundays at 7 pm
and arrives to San Juan on Monday at 8:00 am http://www.colonialtours.com.do/ferries/cabinaint.asp
I call a friend that usually travel on the ferry and he tells me that
they departure from Santo Domingo to San Juan on Sunday and Thursdays.
He say that the schedule is not the same all the time of each week,
I recommend that give them a call.
He gives me the following phone numbers:
809-688-4400 RD office
787-832-4800 Mayaguez, PR office