If you are looking for something a little nicer than the typical Keys type hotel, I like Ocean Pointe:
Key Largo Hotels & Resorts | Ocean Pointe Suites at Key Largo | Tavernier Florida Hotels It's a little south of many of the dive shops in Key Largo but only a 5-7 mile drive to most. However, Conch Republic Divers is very close by.
I've not stayed at the Courtyard Marriott in Key Largo, but many SB'ers have and it is located right next to Rainbow Reef Dive Center, so you won't have to drive at all.
When I go to the upper Keys with dive buddies, we usually stay in dumps or camp. If you're looking for cheap and clean but not luxury, I stayed at the Hungry Pelican with a buddy in July. We only slept there since we dove all day and usually were out somewhat late eating dinner/having a beer or two and were beat by the time we got back to the hotel. However, I doubt I'll ever take my wife there.
The Pelican - Vacation Cottages, Key Largo, Florida - 99340 Overseas Highway, Key Largo, FL 33037 - (877) 451-3576
The last thought is Amy Slate's Amoray dive resort. I've not stayed there or used the dive boats, but they provide both
In Key West, my wife and I stayed at the Coconut Mallory a few years ago and had a very nice time. Like many condo projects, some of the units are nicer than others and we got a recently re-decorated unit that was lovely.
Coconut Mallory Marina & Resort, Key West - Studio, 1 & 2 bedroom Condos for Rental Note that diving in the Key West is not as good as Key Largo, but there are a lot of other topside activitites if the weather is bad..... anywhere from bars/restaurants to shops to museums to historic sites.
It might be too late to make a reservation since they fill up fast, but the cabins in Bahia Honda State Park are decent. Not luxury, but a good deal. My wife and I stayed there a few weeks ago and woke up to see a sea turtle swimming in the lagoon every morning. One of the view decent sand beaches in the Keys is located in the park plus they have a snorkel (not scuba) boat right in the park. You can also rent kayaks. That particular trip was not a diving vacation, but we did head down to Key West one day and I dove the Vandenberg with Captain's Corner.
Have fun on your trip
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