We like the suites of Key largo (key west inn). They are right in the marina. It's not the nicest place but they do have some benefits like kitchens, two bathrooms, upstairs room with bathroom, downstairs sofa makes into a bed and has it's own bathroom. Each unit has a screen porch that overlooks the marina and is a perfect place to dry your gear before you pack it up and head home. We always seem to pay 99$ per night and if someone doesn't mind sleeping on the sofa-bed it can be half that. Again, these are not the nicest places but they are clean and the screen porch for gear makes this place my favorite in Key Largo. Almost forgot, the units are elevated and there is parking underneath, helps keep the car a little cooler in the FL head.
I just have to give a shout out to Jeff owner of the HMS Minnow in Key Largo. The Minnow is a 26' parker setup for a six pack. He is usually first out of the Marina in the morning so you get your choice of balls. The parker has a fin ladder in case you prefer those. Two tank dives with weight run 80$ and NOX is another 9$ per bottle. I have done over 30 dives with Jeff in the past two years and would not consider going out with anyone else. The main reason I bring this up is Jeff has special rates with the Key West Inn.