NYGM is another "super mod" like GWX. You can't use them both on the same game install.
Whether or not it's better than GWX is a purely subjective matter - I haven't played it yet, so I can't say in what ways it's different. There's probably a sticky thread on it in the Mods Workshop forum where you can find information about it and ask people who use it what they like about it and why.
SH3 Commander is a stand-alone program that you use to
1) start and manage a career, a crew, and the accompanying patrol logs
2)activate/deactivate various gameplay options that are not otherwise available (or that Commander makes simpler to use)
3) launch your preferred install of the game once you've done those things to your satisfaction in the Commander interface
Some of the things you can do in Commander:
- adjust water clarity, wave height, time compression defaults, gun reload times, days in base between patrols, and add real ship names and cargo info to your patrol logs
- promote, dismiss, and award qualifications and decorations to crewmen with far more flexibility than the game interface allows
- choose from a variety of "fatigue models" for your crew, including "no fatigue," which eliminates the need to hold their hands and lead them gently to their bunks every time a shift ends so they don't get all tuckered out
- select/deselect options that will make your SH3 experience more or less historically accurate depending on preference
- launch the game in either single mission or career mode with all your preferred options added to the game
If you're like me, you can even print out a copy of your personnel file and crew list after each patrol, and spend a good bit of time going over them deciding who gets a promotion or a medal, so you've got administrative "paperwork" to do when you get back to base... just like a real kaleun.