The two top guys--Frankie and Cicci--were in police custody. The Rosatos, who would have taken over, were on the lam following the shootout with the police. I'm guessing that nobody was in charge for a while. In Cuba, Michael says to Roth, "Who had Frank Pentangeli killed?" That means that he knew about the incident (although not about Frankie's survival) and may have designated a successor for New York, or put Tom in charge temporarily.

But keep in mind that Frankie's regular liaisons in the Police Department may not have been the ones who knew he'd survived (the arresting officers kept it secret). And even if they did, they'd have no incentive to tell Michael or Tom because Michael and Tom weren't paying them off--Frankie was, and he'd turned rat. When Tom said, "Our contacts with the NY detectives said he was half-dead..." he probably meant contacts from the old, pre-Nevada days. And by that time, the cat was out of the bag: Frankie was going to be the witness against Michael in less than a week. No more secret.