Yes, the sole manipulator can always log the time as PIC if he has the appropriate type rating. Part 121/135/91, etc, is irrelevant, because Part 61 applies to everyone.
However, that sort of PIC time is probably useless to you in your career once you reach the Part 121 stage. Others advise you not to log it as such and some airlines specifically ask you to exclude such time from your PIC totals.