Usually noise is from underexposed picture, that mean you must more light :-D
yes, for me Neat Video is the best on market, i use it from over 10 years, i tested many others, but nothing is so good and neat (sorry for words' joke) like it.
the best way to obtain it clean is shooting a target picture (youcan print from neatvideo website picture) before every different shooting, everytimes you change white balance, iso, iris setup you shoot a target, or at least a black (with cap on) sample of noise.
if you sample noise structure from black or better from picture target you can reduce at best without sacrifice real dectail.
other way to work better is to use magic lantern, record more high bit rate, to avoid that noise is ruined from h264 compression.

It can be useful, if you have a good upsampling software, that upsampling undersampled channel like in 4:2:0 sampling.
too many people underestimate how bad color sampled his video until they grade it, and how bad most of software manage it.
More saturated picture you have captured, more important is to upsampling correctly to avoid problems and banding.

prores is free from maverick to upper Os under mac.
i'm cineform owner, commercial version that allow also to have raw video from raw file with active metadata to manage all correction and setup.

h264 = interpreted codec, that mean different os, different decoder slitely difference of what you can see from a same file.
prores = only one decoder time, verytime you see same result.
h264 4:2:0 upsampled to a prores 4:2:2 10bit preserve better original quality and allow to push a bit more with grading without enhance blocking and digital defects.

tons of answers...
i try to be shorter :-P
i'm director, but i'm also a tech expert.
- raw vs prores on blackmagic cinema 2.5k give you very different quality due the quality of scaling and debayering in camera. raw is a lots better.
- shooting raw is like shooting in film, you must think before to shoot, but... 240 gb card is since 24 minutes, a tons of shooting on set... and actually a 480gb cost since 200$, that mean double of it.
i think that raw shoot is an help to avoid to waste shooting ratio ;-D
- shooting raw is simple, and daily and backup can be done from a simple but professional software called "raw4pro", it build also proxy for editing.
- raw vs prores is a lots of space in post to push highlights lower and shadow upper, especially if you shoot in a very complex situation, in external situation where is more difficult to control light.

in 2013 i worked like dit and help director for a full workflow with a 2.5k bmcc full feature lengh movie, 14 tb of data.
Actually i own bmpc4k i most of time i shoot in raw, with exception of theater or similar events.
For me lower is the budget more is important to shoot raw and move decision, working and more in post where you can have more time to massage picture. If you not need post, you can apply some lut, and if light and shadowing are good on set, you must do few work in post, but if you need to massage that picture that you cannot have enought time to manage on set... you have room to do it.
To be honest, a DOP that insist to shooting in raw is understandable, but.. he must know a workflow to manage files, or have a good dit to follow him in that workflow.
i reed to later the date of original post, and probably, i hope for you, you just did the movie.
If you are interest to some tips to manage raw for next movie, i can share all tips that i learn in these last three years, ask me, i'm happy to share what i learned.

Hi Juandi, i'm old user of gh2, i tried different lenses on it, i builded a small set of nikon lenses be cause i like a lot their light renditition. Later i goes on gh3, then actually i'm on bmpc4k and use alternated set of L series canon and my old but good nikon set.
I have many old ('60) lenses and when i close them one stop or two are sharpen than my L series.
The big difference is not in sharpness but in coating treatment, that mean if you have light that hit lens laterally one coating lens give you less contrast and some color change, but is something that i like, and if i work correctly, i not have light leaks, i use mattebox. If i work run and gun i pay attention to it.
I used ai 1.2 lens from a friend, i liked a lots. I have a 1.4 50mm and 1.2 is sharper than 1.4, the big difference between these two lenses are related to coating, that mean when you shoot in low light, 1.2 iris mean that you have a small halo around lights points. you close one stop and all is ok, a more modern lens have multicoating layer that reduce it and is clinical sharper.
remember that if you not choose a good hack like flowmotion 2, sharpness of video is not enought to see difference between these kind of lens.
if you search a good and sharp lenses i can suggest also minolta rokkor MD 50mm 1.4, that you can find around 80$ and is far sharper than nikon 1.4 (i have both).