A common thread was that these were labs that were joint between the university and a UARC or FFRDC. Academic grant funding doesn't usually include engineers, only PI and students, but FFRDC/UARC funding is different. So look at Johns Hopkins/APL, Penn State/ARL, Georgia Tech/GTRI, then (very importantly) look for labs run by a PI with a faculty appointment at the university.
A friend of mine worked at Hopkins for a few years, did interesting stuff, and walked out with a (free) MS afterwards.
I really do think lab composition's tie to grant wording (if the grant says support for three grad students, you get three grad students, not two grad students and an engineer) has a huge influence on how labs are structured, including why grad students end up doing jobs engineers "should" be doing.
A friend of mine worked at Hopkins for a few years, did interesting stuff, and walked out with a (free) MS afterwards.