Hi, Kim! Thanks for visiting us here on the Disney Parks Moms Panel.
Your boys are going to love discovering all the clues that lead to the treasure chest brimming with pirate booty on their
Pirate Adventure Cruise experience! Kids often say that the cruise was a highlight of their Walt Disney World vacation.
There are a total of four Pirate Adventure Cruises offered, each featuring a specific story line (but pretty much the same booty and snacks), which depart from Disney's Caribbean Beach Resort, Disney's Grand Floridian Resort & Spa, Disney's Port Orleans Resort - Riverside and Disney's Yacht Club & Beach Club Resorts. Since your family will be staying at Caribbean Beach, I think it's easiest to have your kids go on the cruise that departs from your resort, if only for the sake of convenience. The cruise lasts about 2 hours, so while your boys are off scouting for treasure, the rest of the family can explore the resort, have a snack or just kick back at the pool.
Now to answer your question about Extra Magic Hours (EMH)...my advice is to take advantage of Morning EMH if - and only if - your family are early risers and can get to the park by the early opening time (usually 8:00 AM). The theme park with Morning EMH will get quite crowded by lunchtime, so if you've got the Park Hopper ticket option, I would suggest hopping over to a different park for lunch and afternoon touring. Personally, I would avoid any park offering Evening EMH unless there are teens in your family. In my family's experience, we have found that it is best to skip the park with Evening EMH and visit the following day instead when it is usually less crowded.
Wishing you a magical, treasure-filled vacation!