In Key Largo, the best bets are Neptunes and Kellys. Neptunes has a small beach where you can pull up on and the rates at both are usually much less than Amoray.
IN Marathon, there is a host hotel that offers pretty good rates. Otherwise stay at the Buccanneer where we used to stop and stay before their office and restaurant burned down. They still rent rooms at very low prices.
As for Key West.., I don't have a clue.
Rick