The difference is a matter of taste, they give somehow different gameplay. Probably you could say that NYGM makes it a bit harder in your side (Own sub repairs, crew management...), while GWX makes it a bit harder in the enemy side (Escorts are better). Might be just a personal impression from me, though.
What you can't ignore is that GWX ships superior graphics, aditional flotillas and still is supported as alabour of love in this forums, while NYGM was discontinued and only a lone member does some minor updates/fixes from time to time.
That said, I'm using normally NYGM instead of GWX, though the reason is mainly that I started with NYGM long ago and don't want to get used to something else, as I like it. For 30th Flotilla careers however, GWX is on my HDD
