Date: 201512
Location: JFK.Airport, NY
Weather elements / visibility: Cloudy
Aircraft: Regional Jet 900 (CRJ900)
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Flight phase: Final Approach
Airspace: Class B JFK
ATC / advisory: Tower JFK
Reporter organization: Air Carrier
Reporter function: Captain; Pilot Not Flying
Human factors: Situational Awareness; Confusion; Communication Breakdown; Distraction
Second reporter function: Pilot Flying; First Officer
Anomaly: Deviation - Altitude Excursion From Assigned Altitude; Deviation / Discrepancy - Procedural Clearance; Inflight Event / Encounter CFTT / CFIT
Detector: Person Flight Crew; Person Air Traffic Control
When detected: In-flight
Result: Flight Crew Overcame Equipment Problem; Flight Crew Returned To Clearance
Contributing factors: Human Factors; Weather
Primary problem: Human Factors

Narrative: The 'MDA' was set in the altitude preselect instead of the 'stepdown altitude'.  We were flying to JFK as Co-Captains. My roll was PIC and the other pilot roll was SIC. On this leg; I was the nonflying pilot and the SIC was the flying pilot.  The weather at JFK was marginal VFR. ATC was using the ILS 4R and the RNAV GPS Y 4L approach. We were assigned the RNAV GPS Y 4L approach.   Throughout our flight; I was privately admiring the proficiency; professionalism and airmanship of my Co-captain. He was doing an excellent job in the performance of his duties and his conduct of CRM.  We conducted the CANPA procedure. As we approached the REPRE stepdown fix; the SIC called for the MDA altitude instead of the stepdown altitude. Since we were in VMC conditions; I set the MDA in the altitude preselect without verbal question. I do remember thinking; for just a flash of a second; 'Oh; he's having me set MDA; and he's going to mentally adjust the descent rate for KRSTL (the final approach fix)'.  I then proceeded to observe the VMC conditions outside the airplane; especially noting the surface winds and the whitecaps on the ocean surface; and updated the SIC of my observations.During our descent; we received the 1;000 foot call out from the radar altimeter and then the gear warning horn. We noted that as being out of the ordinary and lowered the gear. Shortly thereafter; we received the low altitude alert from JFK tower. I advised the SIC that we were too low; at MDA and just approaching KRSTL (the final approach fix). About the same time; there was an autopilot trim caution message which the SIC corrected by disengaging the autopilot and retrimming the airplane. Being in VMC we remained at that altitude and continued for an otherwise uneventful landing. Evan though both pilots were completely engaged in the approach and procedure; the assumption was; by both pilots; that the descent would be adjusted for the proper altitude at KRSTL (the final approach fix). Both pilots missed it. If the flying pilot would have called for the stepdown altitude instead of the MDA; 'AND'; if the monitoring pilot would have insisted on; or corrected; the altitude selection for the stepdown altitude; the whole altitude deviation situation would have been avoided.


Second narrative: Distraction caused by the PITCH TRIM caution message on approach.While Descending on the RNAV GPS Y to 4L; we began our descent from REPRE at 2;000 feet. And outside of the final approach fix KRSTL we descended below the clouds and proceeded visually to 4L. Shortly after breaking out of the clouds we received a PITCH TRIM Caution message; and with the caution message I noticed the aircraft begin to pitch up. I turned off the autopilot and got the trim under control. The aircraft was always stable. However due to the distraction we noticed that we had descended below 1;500 before KRSTL. We were on the visual approach; so we corrected for the descent using the PAPI. We didn't descend below our minimums at anytime until we established the aircraft on the PAPI. We landed without incident and proceeded to the gate.


Synopsis: During the JFK RNAV (GPS) Y RWY 4L; a CRJ900 crew descended below the minimum altitude at the FAF and received a low altitude alert from JFK Tower.