Hi Kim,
Unfortunately there are no restaurants in WDW where you can dine with pirates, I hope they add one one day as I think it would be a great addition to the character meals that they already have!
You can however dine with lots of characters that aren't Princesses. For example a great time can be had at the Garden Grill in Epcot, here you get to dine with Mickey, Pluto, Chip & Dale in a restaurant that rotates through part of The Land ride which is pretty cool. Your boys may be a little old but if they still like the Hundred Acre Wood characters then book a reservation at the Crystal Palace where they can dine with Winnie The Pooh, Tigger, Piglet and Eeyore. Or how about dining at Chef Mickey's with the main mouse and his friends.
There are lots of options for boys and you can see a full list by clicking
HERE and then choosing character dining from the drop down list on the left hand side titled dining experience.
Have you considered any non-character restaurants? My children love dining at the Sci Fi restaurant in Disney's Hollywood Studios. Here you get to sit in an open topped car whilst watching old movie clips on a big screen, just like being at a drive through, it's so cool. Or how about the Coral Reef in Epcot where you dine beside a huge tank with fish, sharks and turtles swimming by? You can see those restaurants and lots of others on the link above too :-)
I hope you find something that fits your families needs and once you've decided you can book either online (again use the link above) or by calling 407-939-3463.
Have a great trip,
Jo