It took just eight minutes for Bradley Wright-Phillips to open the scoring at Toyota Park when he tapped in from close range after Chicago failed to deal with a corner.
Wright-Phillips nearly added a third before half time but his shot was saved by Alec Kann.
Chicago pushed for a goal in the second half with Gilberto and Matt Polster both seeing shots saved.
David Accam then hit the post after volleying Polster's cross toward goal.
Gilberto did grab a consolation goal in the 78th minute when he finished acrobatically from seven yards.
Harry Shipp's attempt to equalise five minutes later was beaten away by Ricketts.
The final whistle went just in time for New York, with Chicago Fire in the ascendancy, and they will now turn their attentions towards the playoff semi-final next weekend.