If the deal goes through, the current B-Mets owners are expected to purchase the Class-A Batavia Muckdogs of the New York-Penn League, which is not affiliated with the Mets (the Brooklyn Cyclones are their New York-Penn League affiliate).
The Mets affiliation agreement with the Binghamton club expires after 2012 and, according to Adam Rubin of ESPN New York, their Double-A affiliate could be in New Britain, Connecticut beginning in 2013. The Mets have been affiliated with Binghamton since 1992.
However, B-Mets President Michael Urda told the Binghamton Press-Sun Bulletin:
"The Binghamton Mets have not been sold, and we have not been contacted by anyone interested in our club," Urda angrily said. "There's 12 teams in the Eastern League and we have to address it every single week ... Enough's enough."[line]
In September, 2006, the Mets announced their 38-year relationship with the Tidewater/Norfolk Tides had concluded, and that they had reached a two-year affiliation agreement with the New Orleans Zephyrs for their Triple-A team. After the conclusion of that agreement in 2009, the Mets signed a two-year agreement with Buffalo and became affiliated with the Buffalo Bisons. In 2010, that agreement was extended through the 2012 season.
For more on this, check out Toby Hyde's post to Mets Minor League Blog.