Two points here. One, shutting down Mueller will likely have no effect on the Federal investigation currently happening in New York. Mueller has no jurisdiction at the SDNY, and therefore no control over the investigation into Michael Cohen.
Two — well, I’m going to let the Justice Department’s own website explain:
What are federal crimes?
There are many federal crimes. Some federal crimes involve narcotics, bank robbery, fraudulent activity that affects interstate commerce, wire fraud, mail fraud or tax fraud, any crime in which the United States is defrauded, guns, environmental crimes, and civil rights violations. Some crimes may violate both state and federal laws, such as bank robbery. In these cases, the local U.S. Attorney's Office works closely with state and local law enforcement officials to determine whether a case will be brought in federal or state court.
Emphasis mine.
I think there’s an excellent chance that Cohen’s files will reveal crimes by either him or his client that can be prosecuted in either federal or state courts. Prosecution by Eric Schneiderman’s office means no Presidential pardons; it means, thanks to Paula Jones, no Executive Privilege applies; and it means that the Eejet has a very serious problem here that he has no means to resolve.