From my experience, Seaborne has a better record than LIAT. I've flown them several times and always took off within 15 minutes of scheduled departure vs. LIAT that is almost alway unreliable. So I'd use that option if you want to layover in San Juan.

A charter flight will probably cost you around $3,000 to $5,000 for a small prop plane and double that for a small jet. If that's within your budget do a google search for "San Juan to Antigua Charter Flights" for links to various charter companies.