FLIR's upcoming model looks like you can twist a knob to extend the lightning plug, so it should handle cases better than either of the existing ones.

Re: camera built into phone case, also worth mentioning that the very first version of the FLIR One was a camera integrated into an iPhone 5/5S case. The obvious downside of this is that if you replace your phone with a new model you can't use the camera anymore. This particular design may have a second lease on life if you go to an iPhone SE, but a lot more people moved to the 6/6S/7/7S which won't be compatible.

Standalone versions have been around for years with a really wide array of designs for different purposes (industrial, security, testing, most recently lightweight UAV cameras). For the standalone cameras you pay a bit more because it can't bum off the phone's screen, storage, input, and all that. The TG165 at $350 looks to be the low end unless I'm missing something. No way to browse their site by prices.

http://www.flir.com/instruments/tg165/