My guess is that since the shooters were from NY, they were part of Pentangeli's crew. But Michael was smart enough to guess that Pentangeli was being set up as the fall-guy for the hit all along.

Notice too how close Freddy was with Frank P. in the beginning of the day, which indicates that he probably held some sway with Pentangeli's people.

Who killed the hitmen out of NY?

Cicci.

Notice too how Cicci rolls over on the family later in the hearings.