As
@Wookie said.
The upper Keys are far better for the large wrecks and all reefs, but you've got a good wreck in Marathon, another in Looe Key, and 2 in Key West. Reef quality drops off as you head south. The Key West reefs are not worth the trouble to get to, especially when you consider the higher expense of staying and diving there unless you plan to do the touristy stuff and be able to tell everyone you were at the southern most point of the Continental USA and browsed the bookstore at the Ernest Hemingway Museum and like to climb lighthouses.
During a recent stay in Key West the hotel prices were astronomical so we checked out vacation homes at a brick and mortar local realtor "At Home in Key West". (I avoid VRBO and similar if possible) and got a good deal on a condo that fit the 6 of us comfortably for about $1150 for 3 nights.
If you aren't into the touristy stuff and were under the mistaken impression that there's 2 days of good diving Key West and you aren't looking to dive the Vberg or Cayman Salvager more than once or twice and are flexible with your plans then consider staying in one place, south of Key Largo around Tavernier and make that your base of operations to branch out to various dive Ops during your stay.
Marina Del Mar in Key Largo is a cheap hotel in a nice location and although it's a bit dated it's neat and clean and you won't be unpleasantly surprised except consider yourself lucky if you get a parking spot near your room.
Marinas Club is south of Key Largo approaching Taverneir and is a nice condo community that will give your group space to spread out and cost the same or less than comparible hotels in the area. I typically dive with Conch Republic Divers in Tavernier and when I was in Key West I used Southpoint Divers. If you're going to do the Vberg for the first time I recommend hiring a DM but be prepared for sticker shock as well as the possibility that after shelling out upwards of $150 per day for a dive guide you might get blown out of the Vberg and still have to pay for the guide as we did which pisses me off because the Captain decided not to do a double dip because of the rough conditions that were troublesome to a few other divers without consulting me- who booked our group well in advance and received a promise that the Vberg would be done twice if at all possible.
I do not recommend Lost Reef Adventures due to their very restrictive and unfair very onesided cancelation policy (they reserve the right to cancel up to the evening before for any reason) yet if you don't give 72 hours notice you're basically screwed and are held responsible for the entire cost of the dive. I've had serious issues with them when booking dives in the past that led to a credit card dispute that they lost.
Looe Key Dive Center will get you out to the Adolphus Busch wreck and a couple of reefs that might be interesting on a good day, I found them to be lackluster and wouldn't recommend any reef dives south of Islamorada but your experience may vary.
Conch Republic Divers:
Dive Portal - Dive Calendar
At Home in Key West:
At Home in Key West | Key West Rentals & Real Estate
Marinas Club Key Largo:
Mariner’s Club Key Largo ™ – Welcome to KeysCaribbean
Looe Key Dive Center:
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