I think you're referring to Patrick Tilley's Mission
I've never read it, but I do remember reading the blurb on the back a loooooooong time ago; it starts out with a man bearing the same wounds as Jesus appearing in modern-day (well, 1980s) Manhattan.
I can't find a description of much of the plot, other than what's given on Patrick Tilley's web page for the novel:
What would you do if, through an unexpected twist of fate and time, you came face to face with Jesus of Nazareth? In the flesh. A living, breathing, three-dimensional figure with a disconcertingly casual manner. When you had pinched yourself to make sure that you weren't dreaming and found that he was still there, would you turn your back and walk away - or would you try to find out what he was doing so far from home?
That was the decision facing Leo Resnick, a smart young Manhattan lawyer, and his girl-friend, Dr Miriam Maxwell. Mission is Leo's record of his encounter with The Man. If you've ever looked up at the stars and wondered what it all means, this is the book you've been waiting for. Mission is the nearest you'll get to the Secret of the Universe this side of the Apocalypse.
The trip starts on Page One. Climb aboard.
Here's an excerpt from chapter 1:
I took a deep breath and looked at the body.
Like Miriam had said, he hadn’t been blown away but he was still a
mess. The man was about thirty to thirty-five years old, medium build,
lean hard body. In general, his features were of the type the police
label Hispanic. He had a swarthy complexion and his skin was deeply
tanned. He had a beard and straggly, shoulder-length hair. Like a
hippie who’d done time on a kibbutz. There was a gaping, two-inch wide
stab-wound in his left side just under his rib cage but the most
unsettling thing was the bruises and lacerations. The guy had had the
shit beaten out of him, then taken one hell of a whipping. The skin on
his back had been cut through to the bone and there were deep raw
stripes on the backs of his thighs as well. It also looked as if his
attackers had beaten him over the head with a nailed piece of wood.
Miriam pointed to his feet. ‘See that?’
nodded. ‘Yeah, what are they - bullet wounds?’
‘No,’ replied Wallis. ‘Somebody drove a metal
spike through them. Through his wrists too.’ He picked up an arm and
I swallowed hard. ‘Jeezuss!
What kind of people would do something like this?’