I would take DCA-SJU-EIS over DCA-STT ferry to EIS every time for ease. We go DCA to STT to stay land based on STT and then DCA-SJU-EIS to get to sea base for chartering. The code share costs more but if there is an issue the originating airline (e.g. Jet Blue) takes care of it. When I take families we typically code share...when we go with a bunch of guys we usually book separately with Jet Blue to SJU and then typically IC to EIS as costs are less pp....if there is an issues they can draw straws and we pick up the short straw at Trellis when they finally arrive

We have had too many ferry issues on the front end with DCA/STT/ferry and STT airport can be more difficult/crowded than SJU for the time we fly. Also there are more flight options in SJU to get to the states and we have been "stuck" several times somewhere along the route. Typically there is not a direct flight form DCA to STT either....

Lately we have been Jet Blue to SJU and Island Birds 9 seater to EIS as we have had 9 going which is easy but more expensive...and usually I can get out of sea base that same night. The cost for Island Birds to fly into SJU has gone up so they are offering another airport (Isla Grande) close to SJU which drops the price and we intend to use this on the way home.

If DCA to EIS is cheaper that would be great....but regardless we go to SJU/EIS for charter over STT/ferry.