As seen in Marvel's The Avengers (2012), however, quinjets are a SHIELD fighter jet that can also be used for transport.
This version later appeared in the same capacity in October 2015 in two different issues: Captain America: Sam Wilson #1 and Howling Commandos of SHIELD #1.
Now, I can't guarantee that these are the absolute first appearance of this model. But what I can say is that I've looked at several issues of various series and miniseries between those two dates, and the quinjet always looks like the original model. And every quinjet I've seen since October 2015 has been the new model. The new model also coincides with All-New Marvel Now!, so that makes sense.
That being said, if anyone CAN find an earlier appearance of the SHIELD quinjet, let me know!