When I stop in the DR it's in Puerta Plata (Ocean World) and Samana.
I have not had security issues at with place. But you still must be cautious and use common sense.
The Mona is no big deal as long as you work the weather and follow Van Sant's advice. Don't push it. You may have to wait several days for the right conditions.
Going around the south of PR
can be great, IF the wind direction is just coming offshore. Which isn't all that often this time of year. But there are more places to stop.
I would spend time in Vieques and Culabra before going to St. Thomas. And there is a nice marina at Palmas Del Mar on the east coast of PR
Personally I'd look at leaving from someplace like say Grand Turk or Salt Cay. That way you start out much farther east before you head down and east.
You could jump to Sousa or Río San Juan for an over night break before heading to Samana or further east.