How perfect for your son to celebrate his birthday at WDW, and the pirate cruise, too! Make sure and let the cast members know it is his birthday when you arrive for the cruise. Just an fyi, I actually have a video posted on our website that shows how we celebrated my son's birthday this summer. Make sure and get your son a birthday pin! Chef Mickey's will be so much fun for his birthday, too.
You have some fantastic places to dine, and I'm jealous just thinking about how much fun you will have. If your son is adventurous, you may want to point out to the waiter/waitress at Whispering Canyon Cafe that he is celebrating his birthday (it's okay that it is a day after). When we did this for our son (he was 11), the waitress called all the girls under the age of 14 to come over and sing happy birthday to him. It was an absolute hoot! I don't think they'd do that, but I'm sure that they'd have some age-appropriate fun adventure for him.
Your trip looks wonderful! Have a magical time and enjoy all the beauty of WDW. You'll be visiting the best resorts during this time (GF, WL, and AKL) as well as the events (MVMCP and CP), so you'll be able to soak in all the beauty of the holidays.