I recall this very sketcy premise as being the basis for a novel (or perhaps a short story) back in the mid-90s, or so. I think the apostle Peter also returned with Jesus. Perhaps it was set in the deep South, maybe in the 50s.
Anyone?
Sir Rhosis
Not the one you were looking for, but your posting reminded me of Only Begotten Daughter, by James Morrow which was a very strange and depressing tale.
“The Shack” has God as an Aunt Jemima-esque black woman.
Could this be what you remember?
I think you’re thinking about the TV show Good Times.
The first thing that came to me was The Shack also.
But other than a supreme being coming in African American form; it’s not really what you’re looking for.
Minor hijack, but what did you think of this book? Blew me away.
The Shack is not it; but it is what reminded me of it. My wife read the latter, and it made me recall the one from the mid-90s or so. I believe The Shack was around 2007, so its much too late.
I never read the one I’m looking for; I just recall hearing of it. No more details than what I gave earlier. But I’m positive it was Jesus and St. Peter who returned.
Thanks, anyway. Googling lead me nowhere.
Sir Rhosis
God is Dead by Ron Currie Jr., maybe?
Jesus comes back as a black women who wanders through Somalia, distributing grain, but is killed by a U.S. missile strike.
Edit: Nevermind. That was 2008.
Oh, No, Thou Didn’t!
Hmmm…seems like short story Bucky Goes to Church had a similar plot. I don’t recall it all that well, but it was in an anthology, Metahorror.
Bucky goes and shoots up a church and meets God, who I believe was a black woman.
Winner! Thread ova. 
A. J. Langguth wrote a novel called Jesus Christs, in which Jesus comes back in all manner of unexpected forms. Could you be recalling a segment of that?