When it comes to money laundering, tax evasion, etc. they can also be charged under state law. Trump can only pardon federal crimes, not state ones. The Attorney General of New York has gone after Trump regarding Trump University, Trump's family trust and other matters and he is working with Mueller.
From August:
https://www.politico.com/story/2017/08/30/manafort-mueller-probe-attorney-general-242191