There can be any number of reasons why JA chose Antigua. One possibility might be that it's identifiable enough for her average reader to place it in the West Indies (and likely associate it with slavery and sugar), but it is small enough to grant it a level of vagueness. Unlike a some of the larger islands, readers wouldn't have bits of information and interpretations popping into their heads that would distract them from the storyline. Antigua also seems to have missed out on any military action during the Napoleonic Wars (I looked for references during the last MP group read). Some islands changed hands several times during this period - again being a possible distraction.
If that was one of her reasons for choosing an island like Antigua, I think some of the other posts in this thread give some valid reasons why she decided on that particular island. It is possible she found out something about Antigua's sugar production (vs that of the general area) which made it a better candidate. I can also imagine her drawing on information from her sailor brothers if they had landed there. (Attention to details which wouldn't even occur to almost any other author seems so typically Austen.)
Somewhere else in this thread, a comment was made about Sir Thomas being a kind of "absentee landlord" to his sugar plantation. When the people he left in charge made a real mess of things, he had to step in personally (thus making the trip). I was struck by the parallel of how Sir Thomas was also an absentee to his own household. He left Mrs. Norris in charge far too long, until he awoke to the need to take an active role.
I remain,
Jason E.