Pardon power of the president is limited to federal crimes. Thats why it has been interesting to see Mueller collaborate with the NY AG. It may be an attempt to circumvent Trumps ability to intervene with a pardon.
BINGO! We have a winner. Even a Trump Pardon, which will be viewed as completely illegitimate by most people (because it would be), would only result in Manafort being prosecuted for similar charges in NY State.