Jason, we are doing the same dance in SJU that BVIslandGirl describes, coming into SJU on one airline (Jet Blue in our case) and then jumping on a separate booking for InterCaribbean. The difference is, we will only have a scheduled layover of just under 2 hours in SJU (one hour 50 minutes). Assuming no flight delays, think that's enough time to collect bags and get checked into InterCaribbean? Thanks for the advice!
JetBlue partners with Cape Air. If you buy both flights on the same ticket, you only pay baggage fees once, they transfer your bags and they have to put you up if you miss your flight. Arriving with a small number of other passengers means you are likely to get through C&I faster, too.
