I think it helps tremendously if your kids are not hooked on handheld video games and DVD players. If you can keep those off the boat and concentrate on the boat handling, the sealife, the view as well as the various 'at anchor' pastimes at the end of those short hops they should have a blast. If they enjoy books that's good for the slow/quiet times.
Beachcombing, swimming in warm water, dinghying around, exploring new towns and cultures should be plenty to keep them amused and interested.
Sounds like a great trip! and 2 whole weeks!!
I took my daughter on longer trips when she was 8 and smaller (some on my blog, below). Though I agree with the above...
* Do take DVDs. They are a familiar thing, from home, and can be good when some reassurance is needed. Kids need some familiar. But NOT all the time.
* A 5-year old is NOT going to be interested in boat handling. It's a grown-up thing and they sense that. Maybe the 8-year old, but don't bet on it. It's not fun until they can really drive, perhaps about 12 (which is when they let them be safety patrols in school--there's a reason).
* Every kid loves the beach. They don't really get long passages, beyond a few hours. So do lots of beaches.
* Make sure they have their own "space."
* Remember to be a kid and play with them. If it's going to be all grown-up time (or if they see it that way) there's trouble coming.