There are many islands off Belize that are less visited than Ambergris and Caulker -- several hundred of them.
But all are small relatively to Ambergris and Caulker. Some (including Tobacco and South Water) are just a few acres. Others are literally just specks of sand or mangrove. Many don't have anybody living on them, and others such as Ranguana, Whipray, Cockney, Northeast and other cayes have only one small lodge or hotel. A very few, like St. George's, Chapel, Moho (the one south) and Long (the one near Lighthouse atoll) have more development but still nothing like Ambergris or Caulker. Some of course are part of government parks or reserves.
As a practical matter, besides the size of these islands, a limiting factor is transportation to most of them. There are no scheduled water taxis or flights, and getting to them by boat is surprisingly expensive.
If you are looking for seclusion, parts of both Ambergris and Caulker are undeveloped -- much of far North Ambergris and most of Caulker north of the split.