Corporations can be, and often are, found guilty of criminal violations, which are normally punished by fines, although in some cases loss of some license, or a ban from being eligible for government contracts (partial or total) could also be imposed.
The pardon power of the US President extends to all offenses charged (or that could be charged, as a pardon can be issued for past conduct where charges have not yet been filed) under US Federal law, with the sole exception of impeachment. (There is argument about whether a US President can pardon his or her own acts. No president has ever tried, so this has never been ruled on by any court.)
Article II section 2 paragraph 1 of the US federal constitution reads, in pertinent part:
... and he shall have Power to grant Reprieves and Pardons for Offences against the United States, except in Cases of Impeachment.
The is no exception for offenses by corporations.
A president can pardon a corporation that has been, or might be, charged with a criminal offense under US Federal law, which would remit any fine.
I have not found any case in which a US President has pardoned a corporation, nor in which the validity of any such pardon has been challenged in court. This list of pardons from Wikipedia does not list any companies, but it does not purport to be complete.