It appears that the Bonanno family did regain it's seat on the commission thanks to their current boss, Joe Massino. According to an old ganglandnews.com article, Massino not only attended the last known commission meeting, but hosted it!

Massino was able to stay out of prison since being released in '92 by using some unusual tactics to run things (his brother in law and underboss turned rat not too long ago, so I doubt he will be a free man for much longer). I read reports a while back that Massino would often frustrate the FBI by leaving the country (his usual destinations were Mexico and Italy) when he wanted to talk business with his guys.

Anyway, I highly recommend reading this article on gangland.com, which named Mossino the "Mafia Chieftain of the Millenium."

http://www.ganglandnews.com/column308.htm