Jason - I've done a similar analysis and came up with the same result, more or less. We've been fouled up and delayed enough times by the ferries that EIS is now our go to route. Even if the ferry route is perfect, it ends up costing us at least a half day travel time each way compared to flying to EIS. Granted, its just two of us usually. Totally get it that the difference adds up for a larger group.

This particular trip, I decided not to book 2 tickets, which did cost a bit more. But, considering that I've had to rebook 3 times so far, it was worth it....Delta Airlines was great and made the changes each time seamlessly. Also, there are entry protocols (72 hour PCR test) for San Juan unless you are just connecting flights thru SJU and we weren't sure if we'd have an issue collecting and rechecking our bags.