Earlier quoted context omitted.
At wavelengths which they both observe (~1–28.5 microns; SOFIA goes out to longer wavelengths than JWST), JWST will be far superior in terms of both sensitivity and resolution. For one, the mirror on SOFIA is less than half the diameter of that on JWST ([0],[1], so the resolution is less than half as good and the collecting area is down by more than a factor of four). Even though SOFIA flies above a lot of the infrar…
Indeed, there are a couple of key things to note: 1) JWST has not been launched, yet. 2) SOFIA's wavelength coverage is different that JWST's or anything else that is in the pipeline. So, really, they are complimentary observatories.
Depending on what you mean by "pipeline", that isn't quite true. Work is being done on several far-inrared missions, such as SPICA[0]. I'd consider SPICA to be in "in the pipeline" and it will cover much (if not all) of the far-infrared that SOFIA does. So I wouldn't call JWST and SOFIA complementary; rather, SOFIA is a precursor observatory and a potential technology development platform (for things like SPICA; not so much for JWST, since the JWST instruments are already being built).