I found a resource hacker that lets you use it through command prompt, so I made a batch file that I run that, among other things only I can really use, it changes the NW.jr explorer icon.
First you need to download the aptly-named Resource Hacker.
From then on, all you need to do is make a batch file and put this line of code in it with whatever else you want. In my case, I merge the package.nw and NW.js EXE into one, rename it, etc. Be sure to put it in the directory with your project.
START C:/Reshack/ResourceHacker.exe -open INSERTPATHTONWJS/nw.exe -save INSERTNAMEOFNEWNWJS.exe -action addoverwrite -res INSERTPATHTOICONFILE/INSERTICONFILENAME.ico -mask ICONGROUP,IDR_MAINFRAME,
And that's about it. Try to keep the files all on the same drive because otherwise this probably won't work and will be 10x harder to pull off correctly. I put in italics what needs to be altered for your PC.