Sam's on Court (off of Baltic) or Sal's on Court (off of Degraw). The former has a good amount of space that often looks underused everytime we're there and the later has a a restaurant that is connected to their pizzeria.
You can also try the House of Pizza and Calzone on Union St. in Carroll Gardens. They did a major renovation last year and have a fairly large back room that might work. Not private, but seems like plenty of space for a large group. Plus the pizza is quite good too.