Was John F. Kennedy Jr.’s accident airplane equipped with an autopilot?
According to the NTSB, the accident airplane did have a functioning autopilot and GPS.

The airplane was equipped with a Bendix/King 150 Series Automatic Flight Control System (AFCS), which was approved for use in Piper PA-32R-301 model airplanes by the FAA on November 1, 1982. The AFCS provided two-axis control for pitch and roll. It also had an electric pitch trim system, which provided autotrim during autopilot operation and manual electric trim for the pilot during manual operation.
The AFCS installed on the accident airplane had an altitude hold mode that, when selected, allowed the airplane to maintain the altitude that it had when the altitude hold was selected. The AFCS did not have the option of allowing the pilot to preselect an altitude so that the autopilot could fly to and maintain the preselected altitude as it climbed or descended from another altitude. The AFCS had a vertical trim rocker switch installed so that the pilot could change the airplane's pitch up or down without disconnecting the autopilot. The rocker switch allowed the pilot to make small corrections in the selected altitude while in the altitude hold mode or allowed the pitch attitude to be adjusted at a rate of about 0.9 degree per second when not in altitude hold mode.

According to the same report, at least two different CFIs judged the accident pilot at least adequate in the operation of the airplane’s autopilot.

A second CFI flew with [Kennedy] between May 1998 and July 1999. This CFI accumulated 39 hours of flight time with the pilot, including 21 hours of night flight and 0.9 hour flown in instrument meteorological conditions (IMC). The pilot used this CFI for instruction on cross-country flights and as a safety pilot. On July 1, 1999, the CFI flew with the pilot in the accident airplane to MVY. The flight was conducted at night, and IMC prevailed at the airport. The CFI stated that, during the flight, the pilot used and seemed competent with the autopilot.

Also:

A third CFI flew with the pilot between May 1998 and July 1999. This CFI accumulated 57 hours of flight time with the pilot, including 17 hours of night flight and 8 hours flown in IMC. The pilot also used this instructor for instruction on cross-country flights and as a safety pilot. This CFI had conducted a “complex airplane” evaluation on the pilot and signed him off in the accident airplane in May 1999. According to the CFI, on one or two occasions, the airplane’s autopilot turned to a heading other than the one selected, which required the autopilot to be disengaged and then reengaged. He stated that it seemed as if the autopilot had independently changed from one navigation mode to another. He also stated that he did not feel that the problem was significant because it only happened once or twice.

53N’s GPS was capable of driving the autopilot.

The accident airplane was equipped with a GPS receiver, Bendix/King model KLN-90B. The GPS was capable of presenting moving map displays; bearings and distances to programmable destinations, such as airports and waypoints; airport information; ground speed; and other information. The GPS was also capable of interfacing with the AFCS and the pictorial navigation indicator.

The accident occurred in July 1999. The KLN-90B’s navigation database was not current.

The navigation database indicated that it was effective on October 8, 1998, and that it expired on November 4, 1998.

As to operability

On July 29 and 30, 1999, the avionics were examined at the AlliedSignal/King Radios Facility, Olathe, Kansas, under the supervision of a Safety Board investigator. On October 13 and 14, 1999, a follow-up examination of the navigation and communications transceivers and all three autopilot servos was also performed at the AlliedSignal/King Radios Facility under the supervision of a Safety Board investigator. [P]arties to the investigation were present during both examinations.
The accident airplane’s AFCS was examined. Examination and functional testing of the AFCS pitch, pitch trim, and roll servos did not reveal any evidence of a preimpact malfunction or jam.