I was able to compare an early and a later MGC M4A1 carbine lately when visiting a friend's house. Both were bought back in 2006 and 2008.
The first ones came in a natural HW silver-greyish color, the later ones were black. The later M4A1 “Short” (Commando) version and the "R.I.S." version were black as well. Later black M4A1 Carbines had a sticker "Black" on the box. The last production run that came in a plain box was silver-greyish again, but had the later lower receiver front lugs.
These lugs are interesting. You may notice that the lugs on the black receiver have been modified to the real (reinforced) M16A2 standard, whereas the lugs on the first model were more like the ones on older M16A1.
Claymore has posted pictures of his black model here in the past that features the early “M16A1” style lugs so there are black models with these lugs too. Anyway I suppose you can tell by the lugs, regardless of the color: earlier MGC M4A1 models have the older “A1” lugs, later the “A2” lugs.
The stock on the early model seems to be painted in a silver-greyish color, the later one is shiny black plastic.
I could not find other differences than that, supplied magazines, carry handle/rear sight and extras seem to be the same, as well as the markings. Manuals are dated 2004.
It is up to you which you like more. At first I was a big fan of the black version and didnt like the silver-greyish HW color. This has changed over the years. The natural HW tends to get darker and more realistic by handling and oiling, looking quite good.
For comparison there is a Hobby Fix M4A1 as well. Its color is a dark grey and in some way in-between.
I miss the days when we could get a nice MGC M4A1 for a good price from Japan or HK.
Early version with M16A1 style lugs.
Later version with M16A2 style reinforced lugs.
Two MGC versions, HF M4A1 for comparison.