But since Magneto ripped his entire skeleton out in Wolverine #75 and he grew back... maybe his foreskin can grow back.
Howlett's mutation manifested in his teenage years:
So his healing factor would be taken into consideration when Magneto ripped his skeleton out. However, it's likely he was circumcised before the healing factor kicks in.
However, given that he was a sickly child until after the mutation kicks in (see Wolverine: Origin 2001) but loses all shred of that feebleness as soon as he gets his claws, we can speculate that the healing would cure anything already there, so it would stand to reason that the foreskin would have healed.
Unfortunately, the exact specifics of of the extend of his healing factor are not 100% clear. For instance, in Age of Apocalypse, he undergoes extensive torture at the hands of Dark Beast (I think, it might have been Mr. Sinister) and while he has his healing factor, the extent of the damage (implied to be a cellular mutation) could not be restored. On the other hand, he's survived atmospheric entry on Breakworld (See Astonishing X-Men around 2004-2005) where his entire skin appeared to have burnt off and regenerate.
I'd say that since his penis probably burnt off with the rest of him at that time, it would have had to rebuild itself, complete with foreskin.
Y'know, two days ago I was saying how I don't give a shit about Batman's dick, yet I just went down a rabbit hole for Wolverine's.
After thinking about this for a while, I think that most mutant powers manifest at puberty. So I think since his mutant powers would not have come into being until after he was circumsized at birth.