I've been uploading my animation videos encoded with PhotoJPEG (95%) but in some cases it produces horrible banding on gradients that cannot even be fixed with some noise.

So now I'm looking into using another high quality codec that is accepted at all agencies. I'd like to use QT Animation or PNG but I reckon I can only use that if I have an alpha channel/transparency. ProRes also isn't an option unless someone knows how to convert to ProRes on a Windows machine (I've tried ProResConverter script for AE but it didn't work properly).

That leaves me with MJPEG but Pond5 doesn't accept that. H.264 isn't an option. So I need some advice here.

Banding is horrible with PhotoJPEG especially with ultra clean animations. There are ProRes plugins for Windows just a Google search away, and will solve all your problems. 
I'm on a mac so I can't recommend one, but they're there.

I tried another ProRes plugin (AfterCodecs) which allowed me to use the ProRes codec. However I still get banding issues (ProRes 422).

So far, QT Animation (@ 16 bpc) gives me the cleanest gradients with the least amount of banding.

Are you using 422 HQ, 422, or 422 LT? 422 HQ is pretty good, try to avoid the other ones. Also make sure that you work in 16bit/channel mode in After Effects, to get the most out of the 10bit/channel that ProRes can do.

The frames you posted are very dark. At first I though they were just black. Is your display accurate? There aren't that many brightness steps so close to black in most codecs, so if your display is boosting that range back up, you get extra banding.

Finally, if still necessary and after you fixed all other problems, you can add a tiny bit of noise to make the last banding go away.