I would guess that with the leadership changes necessitated by Frank Cali's untimely death, with the shelving of Cammarano and Zancocchio with the Bonannos, the typical chaos atop the Lucchese regime and the irrelevance of the Colombos, the only real prize left in New York of any real value and the only real uninterrupted reign which may have given the government enough time to build a case of any magnitude would be a case against Barney. Whether or not this is happening, who knows. But if I were an ambitious DA in New York I'd think Barney is the only prize worth having.
I like the guess on Joey - have to assume that the authorities would love to take down someone as visible as him.