Couple of issues beside Hurricanes!
Most homes are not able to be rented for less than 28 days, a Monroe county ordinance, so you should check to see if they do weekly rentals.
Captain Pips rents boats (both CC's and Flats) in Marathon, they also have lodging, but I cannot speak to what the lodging is like.
Further down on Ramrod Key, Dolphin Marina has some efficency rental units and rents what I recall are 22ft Angler CCs with 150 and 200's yamahas.
Try the site VRBO.com, vacation rentals by owner and then search the Keys.
LD