If by "premier," one means "the one that set the standard," then it is Marillion hands down. However, if by "permier" one means "today's best," then subjectivity enters the picture.
For my money, the five best neo-prog bands out there (and my "neo-prog" is not the "official" definition, but rather any prog band that entered the picture after 1985, but specifically "filters" the seminal "classic" prog bands) are:
Marillion. The superb "Marbles" shows that they are still very much in the game. They "wrote the book" and they are getting better again.
IQ. "Dark Matter" is certainly brilliant, but so is "Seventh House." Even "Ever" is excellent, as is most of "Subterranea." Simply some of the best neo-prog out there.
The Church. Has everyone forgotten that "Forget Yourself" got the highest ratings on this site (and many others) of any album of 2005? After "Hologram of Baal" and "After Everything Now This," they put out the best album of their career. And the new one, "Uninvited Like the Clouds," if not the masterpiece that FY was, is nevertheless an extraordinarily creative album. These guys are simply amazing.
Pendragon. Although I continue to have a problem with their vocalist, there is no question that their output is excellent.
Porcupine Tree. Yes, I know: they are not "officially" neo-prog. But that is how I think of them, and so they appear on this list. And rightfully so, especially after the superb "Deadwing."
I would also have included Spock's Beard, but I no longer think they are making music as good as they did when Neal Morse was still with them.
That's my two cents. Or maybe five cents.
Peace.