Hi Lisa,
Pirates League is a lot of fun, and it's a great alternative to Bibbidi Bobbidi Boutique. Although no one will ask you for proof of your child's age, the makeover is geared for guests over the age of 3.
That doesn't mean your son will have to miss out on the fun. He can get a cool hairdo at
Harmony Barber Shop on Main Street. They can add hair gel and colorful confetti, or there's even a first haircut package that includes Mickey Ears and a certificate. Reservations can be made by calling (407)939-3463. That's the Disney Dining number, but they will also help you make reservations for this as well.
There are also face painting stations all around Walt Disney World. They do amazing work, quite quickly I might add - which is perfect for little ones. Some of the booths even offer a pirate themed option. I know I've seen it at Downtown Disney, and it doesn't hurt to ask at any of the face painting booths.
Hope this helps. Have a magical vacation!