There is no direct connection from Newark to Harlem. However, you can take the train to 34 St - Penn Station then take the line 2 subway to 125 St. Alternatively, you can travel from Newark to Harlem in around 21 min.
How to get from New Jersey to Harlem
From Newark Penn Station train to 34 St - Penn Station then line 2 subway to 125 St. 37 min $10. From Newark taxi to Harlem. 21 min $119. From Newark drive to Harlem. 21 min $2.