Anton Tinnerholm joined Mitrita as the team co-leaders in goals as he scored his fourth of the season while captain Alexander Ring notched three assists for NYCFC (7-6-2, 23 points), who netted three first-half tallies for the second time in as many games.
Sean Johnson finished with three saves as NYCFC improved to 6-2-2 in their last 10 matches to move into fifth place in the Eastern Conference.
Morgan scored in the 27th and 38th minutes before Mitrita capped his two-goal performance in the 43rd minute to give NYCFC a 3-2 lead.
Mitrita was able to cap a lengthy run by weaving his way into the box and unleashing a shot that caromed off an Inter Miami defender and into the net. The goal was the fourth of the season for Mitrita, who also tallied twice in NYCFC's 4-0 romp over FC Cincinnati last Saturday.
NYCFC wasted little time gaining the advantage on Saturday, courtesy of a pretty set up by Ring. The captain lofted a cross that a sliding Mitrita sent over the extended left arm of Luis Robles (two saves) in the fourth minute.
Miami forged a 1-1 tie in the 27th minute, with Victor Ulloa deftly sliding a neat pass to an unmarked Morgan. The 24-year-old Morgan made no mistake, unleashing a right-footed shot from inside the box that sailed past Johnson.
Tinnerholm wired a left-footed shot from just inside the box that sailed past Robles in the 35th minute for his third goal in his last five matches.
Morgan answered three minutes later by rocketing a blast just inside the top corner for his second goal of the night and fourth of the season.