I think at one point I did try and have seen someone else try printing ninjaflex in a gen5 and had limited success.
As I remember it, I could load filament and even started printing a test cube but it failed mid print.
The problems are numerous in that you really cannot print ninjaflex fast and since it wants to buckle, the entire feed and guide path is pretty much a custom design requirement. The real kicker was that at the time, changing some settings in the profile where not affecting the actual print file and so I never felt i had good enough control to tune to make it work with ninjaflex reliably.
My test said sure, you might get a test print or two off, but I'm betting the first real important project you need to print is going to result in frustration.
Given the cost of Ninjaflex, you don't want to waste it.
Net- I say it doesn't work. I'm sure someone will chime in and say opposite and maybe through some miracle the new firmware and software might let you better tune but I wouldn't hold my breath waiting.
Sorry, I've all but given up on MakerBot period.