Ok, your best bet is to fly to St. Thomas. Instead of possible problems connecting at the San Juan airport, step out into island time in paradise! Start your vacation by taking the ferry--consider the ride across the water a part of your vacation.
The St. Thomas ferry dock is both near the airport AND near downtown Charlotte Amalie, premier cruise ship destination and home to some of the best shopping in the Caribbean! A nice place to have a travel snafu!
You can also arrange air transport by charter (see Local Airlines) from St. Thomas and San Juan. This usually works better financially with a larger group. St. Thomas Air has a good reputation for local flights.
The San Juan airport. Be sure to check in and get your boarding pass for your connecting flight as soon as you arrive unless you are interconnecting between American and American Eagle (and it's still a good idea). San Juan is a major interconnecting point and has suffered a lot of problems.
Also, have a carry-on bag with your travel essentials, "covering" the possiblity of an unexpected overnight stay without your luggage.
Experienced travel agents recommend booking in a minimum connecting time of two hours, instead of the expected one hour, at the San Juan airport.