That's easy.  Many would come to follow him, and the pope would declare him to be the anti-christ. Then every street corner will have a bible being waved in the air with someone blabbering "it was foretold. REPENT!! For the kingdom is at hand. The true Messiah Jesus is coming."

Gee Bum, maybe they will read this one day and declare me to be a prophet.

You and me both...

Nah, they wouldn't know the difference because they'd all land in the rural areas that Bill Hicks did his UFO Tour in, the ignorant farmers would all grab their shotguns and head out to the fields for fear of being abducted for scientific experiments and various acts of probing.

Upon seeing this display of gross misconduct and impending violence, the only thing the alien would say would be "Jumping nigelsnort, I'm getting the beejumpbay out of here!"  *cosmic dust trail*

What if the alien didn't want to do that? What if the alien wanted to pretend to be a god or jesus or what ever; the motive is the reason why I asked this question. What if they didn't use a spaceship to land out in BFE? They instead came down on a beam of light or a burning bush? trumpets with angels and wings and all that shit.

The problem with all that is people believe in all sorts of whacked out shit; most of which are purely fantasy and we know it.  For example, most of us wish things like big foot were real, the Loch Ness monster and unicorns.  Now, if we were to suddenly be presented with such a reality-shattering opportunity to be in the presence of all of these things, including an extraterrestrial life form that claimed to be the savior our religious folk have been waiting for, everone's beliefs would go right out the window and take a back seat to immediate and near dangerous skepticism even after years and years and years of being so certain of the existence of such things whether it's an agnostic mentality or a faith-based mentality.  We are naturally bound to deny everything spectacular and what seems to be nearly impossible regardless of how strong our feelings are.  It must be a primate reaction in our brains or inferior thought patterns that haven't evolved to a higher degree of understanding yet; who knows?  Maybe our race has been fooled so many times before through scientific hoaxes, bad photography and mistaken objects in the sky that we've developed this overly irrational way of dealing with unbelievable phenomena.  Could be any number of things. 

He would:

1. need to appear primarily human enough to mimick the oft-assumed appearance of the Judeochristian "God" (a la Arrival)
2. also need to descent slowly upon Jerusalem in his... 'vessel'

I've thought about this before... under Philosophy " What would count as absolute proof that god exists"

Its not simply about how Christians will respond, but how would the rest of us response.

The conclusion that ive come up with is that no human can ever be sure its god or some advanced alien. If he shows us love and gives us stuff maybe we could live in a "heaven"-like place for all eternity. It wouldent really matter to us if its god or an alien as long as were happy.

Were ignorant by default.  

To answer the question. No, there is no way in hell a Christian can know the difference and neither could the rest of us.

I believe that there would be a group which said "yep, that's him" and then another group which would say "no, that isn't him - he's a fake"

Then of course you'd have the scientists who'd be there saying, "huh... if your a god why is your space craft hiding behind the moon?" and a bunch of other scientific observations.

If a large quantity of people across the world mysteriously vanished into thin air, then I guess they believed.

The rest of us left behind would be struggling to formulate a large enough nuclear arsenal or otherwise technologically advanced weaponry (nanovirus comes to mind) to counteract the impending doom. According to the Bible, things are going to get hot.

However, since the Bible is missing sections, there is still hope.. Maybe in a missing chapter it is prophesied that our new/old friends (the fallen angels) will lend us some stealthy spaceships to get out of dodge.

The theists would probably believe it. Their first question would be about raptures and punishments to gays, fornicators,atheists, and all the other people they hate. I am willing to bet they would be doing that while bowing and proclaiming messages of love.

There was a Star Trek: TNG episode that used this idea as a story.
Long story short, any species that could come here and convince any substantial number of people of that species divinity based off any Earth religion would be incombatable (read that word again, your brain probably defaulted to seeing incompatible, which doesn't fit the sentence).
I'd be much less worried about a species trying to get us to accept their religious beliefs instead of one that studied ours and used that knowledge to their benefit.