There's only 3 options for diving on Nassau since it's all boat diving. All three operators compete - 2 tanks start at about $115 - slightly less if you buy multi-days. The best I've seen is Stuart Coves offer of 4 dives the same day for $160. Everybody charges a little more for specialty (sharks, Blue Hole etc.) dives.
Stuart Coves on the south side. They run a free shuttle since everything else is on the north side. They list package deals on their website. Orange Hill Inn is about the cheapest but it's not in Nassau so you'd likely need/want a car. There may be a bus also.
Stuart Cove?s Scuba Diving Bahamas Nassau Dive Vacations Thrilling Shark Adventure Dive - Packages
Bahama Divers is just across the bridge from Paradise Island - location of Atlantis - the expensive mega-resort.
http://www.bahamadivers.com/ However there's both a Best Western and a Comfort Suites on P.I. also - since they're not beachfront, they're more affordable. Probably around $150. At one time both operators offered a dive package deal with Comfort Suites. CS also has arrangements with Atlantis so you can use some of their facilities as well - it's about a 2 block walk.
Both operators pick up on Paradise Island - BD's a five minute ride, SC's a 30-40 min. ride from there.
Both Stuart Coves and Bahama Divers also pick up at the hotels on Cable Beach - there's reasonable options there. The Sheraton Nassau is recently refurbished. There's also the Wyndham - it's always?? on the low side. Other less expensive hotel options I know of - but not stayed at - are Nassau Junkanoo Beach, Towne Hotel, Coco Plum - some in less desirable locations. Some parts of Nassau aren't overly safe at night. Junkanoo Beach is old, it was there mid-80's when we cruised there.
Paradise Harbour Club on P.I. is affordable also - not sure why. If I had to guess it's because they're near the golf course away from Atlantis. They're small suites under $100 - that's a deal for that area. It's on a marina - if you get incredibly lucky it's near the marina where Explore keeps their boat - IDK though. If it was, that's about the closest you'll get to "clean hotel close to a dive shop". If not check to see if anyone will pick you up there.
The third dive operator - Explore Scuba - is on Paradise Island. They're fairly new.
Home | Explore Scuba Bahamas is the only dive operator located right on Paradise Island, we offer that one of a kind experience.
Expedia seems to list most of the Nassau hotel options, they don't change much.
hth, I moved this thread to the Bahamas sub-forum for better response.
What Doc said ^^. The Bahamas ain't cheap. Wait till you price food...
If you're not set on Nassau maybe consider Freeport also. Bell Channel Inn is an affordable option with their own shop/boat onsite. UNEXSO is similar but slightly higher priced. I think there's other lodging options near UNEXSO - they're in Port Lucaya. The other Cove's operation is out at Old Bahama Bay resort but that's a 45-50 minute drive back to town.