I just got married in Islamorada this November. However, when I was looking for venues Cheeca Lodge was not an option since they were closed throughout most of 2009 due to a fire on January 1st. They just reopened and I know Cheeca is the best large family-friendly resort in Islamorada... perhaps the best large resort in the Keys. Casa Marina resort in Key West would be on about the same level.
If you're having a smaller wedding with no children, you might want to check out Casa Morada and/or Little Palm Island. These are not children friendly though and Little Palm Island is incredibly expensive.
You may also want to consider a large private estate wedding, which is what I had. I had complete control and no resort "rules" which I loved. Islamorada has a large number of beachfront estates that are available for rent (Key West also has large rental houses, but they are generally not beachfront or wedding friendly). Visit Vacation Rentals Florida Keysto look at some of the estates that are in the area. I had my wedding at the Island Palms Estate.