Especially for West coast trips (I used to commute to Seattle weekly), I highly recommend flying to EIS. The ferry gets you into an island mode a little faster but after traveling so long I really just want to get there. Flying thru SJU to EIS is now my preferred route. I prefer to staying in the more efficient airport system instead of transferring to the ferries, there are multiple carrier options in case something goes wrong, no dealing with the crappy airport in STT, much better/reliable TSA Pre-check and Global Entry options, multiple food/drink options for the layover, etc... By the time I factor in taxis, tips, ferry cost, and baggage fees I find EIS to be the same cost.

From Seattle, I would break the trip into 2 days because I needed to work on Thursdays at least part of the day. Thursday was Seattle to Atlanta; stay overnight at one of the airport hotels connected to the Sky Train. Friday morning, first flight to SJU, then a connection to EIS. Was usually on the beach for lunch.