I have dove with both Xanadu and Caribbean Divers and each have positives and negatives.
Xanadu, which is located at the Xanadu Resort is much closer to Freeport (Sea Island), and is a larger operation, offers more trips, shark feedings and nitrox. They have an experienced staff and offer a full range of training (I completed my nitrox cert with them) The down side is their boats are old and suspect. On my last trip with them, the boat broke down and we almost had to be towed back to port and they were without a working O2 analyzer, so did not offer nitrox fills. Most recently, we also heard from other divers that their boat broke down again during on our last trip while we were diving Caribbean Divers.
Caribbean Divers is a two man operation, Mr. Knowles and his nephew Jerry, who serves as divemaster/crew. They are located at the Bell Channel Inn across the boat channel from the Port Lucaya Market Place. Although they offer pick up at the Port Lucaya hotels, I don't know if they go all the way over to the Freeport area (I think about 10 to 12 miles). They do have a sturdy boat, so that is not a problem, but they don't always run multiple trips a day and they will cater to resort class divers in packing some trips with resort students and visiting the very shallow (20' to 25') reefs for a one tank dive rather than the scheduled two tank at the medium reefs. They don't do an actual shark feeding dive, but instead observe the UNEXSO shark feeding from near by. Also, male divers are enlisted to help with the loading and unloading of the air tanks (they don't handle nitrox) That said, I really had alot of fun diving with them and wouldn't hesitate diving with them again as they are quite reasonable on their package rates. When staying in Port Lucaya, I would recommend them over UNEXSO (too expensive).
I have not personally dove with Grand Bahama Scuba, but many people, including Tavi, speak highly of them, so I figure it is probably a good operation. They, like Xanadu, are located near Freeport (and your resort) and so would probably provide free transportation. I don't think you could go wrong with them.