Assuming you're not interested in the 3-4 day liveaboard trips some of the FL based operators offer I'm reliably certain you've found the only sub-$1000 option in that region.
The next least expensive option I'm aware of is that Cat Ppalu, Blackbeards "other" boat
occasionally offers extra spaces if someone full-charters the boat but doesn't use them all. $1595 + $110 in port fees.
Charter Sailboat Rates and Schedules - Sailing Charters - Sailing Catamaran - Cat Ppalu
There's also Lost Island Voyages - another Bahamas based boat. I believe they start at $1795. Depending on the trip either out of Nassau or Freeport. There's that ferry that runs between FLL and Freeport but I think it's still cheaper to fly.
Welcome to Lost Island Voyages | Scuba Diving Adventures in the Bahamas | Miami, FL
The Saba/St. Kitts EV trips price out closer to $2K even after the discount when you add in the port taxes/fuel surcharge. $1995 + $115 pt. If they're still adding the fuel surcharge, on the T/C Explorer trip that was $200 more. So your total price is $2010 after the discount. And there's the added expense of flying into St. Maarten and out of St. Kitts or vice/versa. That has to be a more expensive ticket than the hop over to Nassau from Ft. Myers.
One possible Central America option is the Caribbean Pearl II. The full week charter is $2795 but they also offer 1/2 week trips - 5 days/4 nights - embarking on Roatan, disembarking on Utila. In the "smaller deluxe cabin" it's $1380 - 19% Honduran tax included. It's a very nice boat, used to be the Utila Aggressor II till they moved over to DivEncounters booking.
RATES & SCHEDULE
It will cost you $55 to get back to Roatan for your flight out via 2 ferries. Or you can try pricing flying in/out thru San Pedro Sula but when you add in the cost of flights to Roatan and back from Utila that's about a wash since each one is over $100. You can also take the Princess Ferry to La Ceiba for about $22 and then fly/bus from there to San Pedro Sula but that will burn a day and require an overnight in La Ceiba - San Pedro Sula isn't a safe alternative - mainland Honduras being the murder capital of the world currently.
I'd consider adding a few land-based days on in Roatan also, stay in the West End where it's very reasonable - rooms well under $50/nt - hostels if you do that at $10. Food is really cheap and dives run about 10/$300. The ride there from the airport is $25 fixed and everything is within walking distance. Coconut Tree Divers has a good generalWest End info page:
Roatán, West End | Scuba Diving | Roatan, Bay Islands, Honduras | PADI
Or Utila which is almost identically as cheap. Maybe even more so as it's a known backpacking destination. We stayed at an AI there so IDK the "in town" prices. The ferries connect twice/day so there's no immediate need to get back for your flight home. Utila has a small airport and only day flights back to Roatan on a charter basis or to the mainland on a semi-schedule.
Utila Official Site - Utila, Bay Islands, Honduras - Tropical Island Paradise for everything.