We're using (a bunch) of miles to take the trip, hoping to get all 5 of us in first class (thanks to Amex points). The miles for Houston to St. Thomas appear to be almost double the miles to San Juan and there are half the number of flights to St. Thomas. So since the big leg is basically free, our budget for the puddle jump leg is flexible.
I can't yet see flights on Silver Air for our return trip (will open up on Saturday if they follow the pattern used by Delta) so will check them out. I've thought about a charter but coming from SJU, I gather it is a lot more than going from the other Puerto Rico airport. After a long day of flying, hauling luggage through SJU is bad enough without having to also deal with a taxi ride. Sill I'll check out the charter options.