I have found the most economical way to travel to EIS is on 2 tickets. In 2018/19 I probably made 60 trips between Tortola and either Ohio or Seattle. I priced it both ways on every trip and after factoring in the ferry/taxi game in STT the price was always within $100. Usually it was a little cheaper to fly to SJU than STT and then the price difference was the ticket to EIS minus the ferry.

While I enjoy the scenery and the journey on the ferry (and the Petite Pump Room), the overall travel experience is much easier in SJU. The airport itself is much nicer, there is real food/drink service available, the security is easier, they have a real TSA pre-check, a real Global Entry, and and airport lounge with food and wifi, etc, etc.

If you're serious about trying the EIS route, consider booking 2 tickets. The best options from SJU to EIS are Silver and Intercaribbean. Intercaribbean is usually a little cheaper and they have the last flight of the day so if you get bumped or are delayed you have an end of day option. Silver has nicer aircraft and their gate is in the main concourse (next to 2 bars), but you have to ride their short shuttle between the gate and planes. There is always the risk of flying on 2 tickets that a delay on the 1st segment will cause you to miss the 2nd leg but it has never caused me an issue. I did land late once and InterCaribbean had already moved me to a later flight at no cost.