GWX and NYGM
 

Can these two mods run together?

No.
They both are supermods.

If you use multiSH3 you can make two different installations to run each supermod.

I did briefly consider kitbashing them, but GWX isn't available (as far as I know) as a JSGME mod. If you put NYGM on top of GWX, you're going to lose a lot of the hard work that GWX puts into the game.

Can someone tell me if there's a way to get GWX as a file structure instead of a bin?

Point the GWX installer to your SH3 stock install then before hitting install rename the stock data folder
Installer should make a new data folder of the GWX files

I say should as has been discussed before, not tried it myself as never needed to

There is a way actually but you would need access to the skeleton key created by privateer.

The above was created for GWX team only and as such I feel unable to pass it on.

You could always try PMing privateer though.

You can also modify a few files to use some of the major changes in either mod and use a blend.
The focus of NYGM mod is tonnage sunk. The focus of GWX is game play and superior graphics with attention to reality.
Both are great mods with an enormous amount of work and testing. The new additions are also wonderful and improve the game experience greatly.
I suggest you use them both and make your game a blend of the best features.
I should add that there are at least two other major mods that have wonderful features to improve the game experience.

What are they? Is subsim.com the only real place to get mods for sh3? I know I've searched on google, but the majority of the search results are for subsim.

Take a look at www.silenthuntermods.com
I't's a long time ago I've been there.

Check out the SubSim SH3 mod workshop page

LSH3 (Living Silent Hunter 3)
http://www.subsim.com/radioroom/showthread.php?t=159165

WAC (War Ace Campaign)
http://www.subsim.com/radioroom/showthread.php?t=128050

Thanks, I'll check them out.