We almost always book our own air. Even when factoring in the extra night hotel stay, we come out ahead with our party of three. (And yes -- I highly recommend that you arrive in San Juan a day early, even though your cruise won't depart until evening.)
Booking our own air also allows us to schedule the itinerary. When the cruise line does the booking, you have no control over the route, time between connections, airline, etc.
The only time in the past few years that we let the cruise line handle the air was when we were on an itinerary that started and ended in different ports -- but that is not the case here.