I agree, arriving by charter 2.5 hours before first scheduled connecting flight should be fine. The last time I came into SJU on private charter flight from VG we cleared Immigration & Customs at the FBO terminal rather than the I&C location in the main terminal. We had only carry-on and had checked in on line for our SJU/USA Home Airport flight so all we had to do was walk to the main terminal (about a 10 minute stroll) to clear TSA and proceed to the gate for our connecting flight. That whole process took less than 30 minutes.