Both Freeport and Nassau are fun dive destinations with plenty of top side diversions.
Nassau is a bustling city with lots of shopping and Paradise Island (where Atlantis is located) is a very ritsy area with great beaches and plenty of upscale eateries. The Atlantis is a one of a kind resort with the spectacular water park and aquarium, as well as a lavish mall and the biggest casino this side of Vegas.
There are also number of other outstanding resorts and hotels including my favorite, the British Colonial Hilton in downtown Nassau.
While it is a big operation, I like Stuart Cove's, but it may be because I stick to the specialty dives. The DPV wall flying dives take a maximum 6 divers to reefs along the 6000 ft deep trench "Tongue of the Ocean". Needless to say it is an adventure and almost guaranteed to include numerous shark encounters.
Freeport is the other major tourist destination with a significant dive infrastructure. There are basically two areas of tourist activity, one in Freeport near the International Bazaar (home of the islands only casino) and Port Lucaya (shopping, food and bar district with open air bandstand nightly entertainment). Its a little more laid back than Nassau in general and there are much fewer nice resorts to choose from. The major resort on the island is Our Lucaya in Port Lucaya.
The diving is usually very good in Grand Bahama and shark dives are local specialty. My personal experience has been with Xanadu and Caribbean Divers. Both are good operations with their own strengths. CD is basically a two man operation that leaves out of Port Lucaya which is closest to many of the dive sites. They don't offer nitrox and sometimes cater some to resort divers (make afternoon trip a one tank 20' dive instead of a two tank 50' to 60' trip)
Xanadu, located in the Xanadu resort marina near Freeport, on the other hand runs more trips, and offers nitrox (I don't recommend the Xanadu hotel as it is a little run down) While the dive operation is staffed with highly qualified instructors and run the best shark dives I've been on (the hyponotize the sharks by rubbing their snouts) their boats are somewhat suspect and subject to the occasional mechanical failure.
I have heard many good things about Grand Bahama Scuba, but I have no personal experience with them, although I understand that they offer nitrox and will pick you up from your resort.
Also, I have heard quite a bit about the diving off of Bimini, although I have not made the trip yet. It is a little more difficult to get to as only the Chalk seaplanes are currently offering service from FLL and the ony major topside activity is bar hopping.