To my knowledge, some of the earliest would be the Vickers Viscount Model 724, which introduced a two man cockpit to that family, and the BAC-111, which I am pretty sure had a two man flight deck right from the get go (and was in the air before either the DC-9 or 737).
"So powerful is the light of unity that it can illuminate the whole earth." - Bahá'u'lláh
The Vickers Viscount had a two-crew cockpit. (The first civil turbo-prop)
The DC-9 was the twin-engined jet airliner to have a two-crew cockpit.
The A300-B4 FFCC was the first widebody jet airliner with a two-crew cockpit.
The 747-400 is also two-crew.
Actually, some of the airplanes listed here (namely the Sikorsky and Douglas DC-3) may have had some three man configurations due to the need for nav/com radios. Remember in the early days the radios were not user friendly and not always set up for the Captain or First Officer to transmit as they are today. I believe the C-47 flew with a radio operator. On the DC-4, -6 and -7 radio duties fell to the FE.
"When a man runs on railroads over half of his lifetime he is fit for nothing else-and at times he don't know that."