We've done Marathon Key a few years in a row. There's a hotel there called Glunz Beach Ocean Hotel - right on the ocean - basic but very clean and pretty nice hotel suites that can sleep four easily. In Marathon there is the turtle hospital -which kids love, a new aquarium which isn't big but is done right and is very engaging to visit, Bahia Honda is a state park just passed Marathon over 7 mile bridge - one of the best beaches I have ever seen outside of teh Caribbean, SE Asia, etc. Huge flat sandbar area to walk and play in - kids will have a blast. There is camping there but it is often full.

Key West is kind of a bust with our kids - so crowded and hot! Though Ripleys museum is a crowd pleaser. we always snorkel and do a kayaking trip while we are down there too.

It will take you 2 days to get there and back so you'll only be at your destination for 3 days...is that what you are looking for? You can get beaches and shells much closer than FL and Key West

Any advice on what to see, places to stay? Kids are 6 and 8 and we are frugal travelers (so the Ritz is out)! Kids like beaches, sea shells and animals...