Anchorages I find tend to be quiet and often have had to myself:
Double Breasted.
Strangers.
Joes
Jacks
Yankee Harbour
Maybe Big Carter's
Paw Paw (in settled
weather only)
Lower
Fish Cays
Moraine
Umbrella
Hog Cays
Powell
Bay at north end of Manjack, though it now has a cottage in it.
No Name
Spoil Cay
Snake Cay
Bucaron Bay
Pelican Cays (day stop, maybe overnight in settled weather)
Bight of Old Robinson
I second what Vasco said about north being quieter.
Photos of most of the above and a few anchorage maps on my webpage:
www.bahamasmariner.com (still in progress, pardon the mess)