" But we didn't want to pay $300 one way for each of us."
Was just looking at Cape Air, just a little over $600 RT SJU/EIS. Sure makes my EWR/SJU/EIS tix at $495 look like a real bargain.

Did you try VIAirlink? I looked at their website(pretty much worthless) but I thought they had a flight between SJU and EIS. Might be worth giving them a call.