"Will graduate" vs. "will be graduated" vs. "is going to graduate"

Which of the following sentences are correct?

1. He will graduate in May.
2. He will be graduated in May.
3. He is going to graduate in May.

Issue 1: Is the second one grammatical?
Issue 2: There is high uncertainty that cause he may not graduate in May, like fail one course?
Issue 3: In a formal letter, which one is correct?

Besides, I heard from one of my friend whose mother tongue is not English: "I have been graduated from Boston university". Is that one grammatical as well?

I know the second one is passive and not correct but in this article I saw somebody use it. Therefore I am confused.

They are all grammatical. Merriam-Webster gives three definitions of graduate in connection with schools.

transitive verb:
1 a : to grant an academic degree or diploma to
1 b : to be graduated from
intransitive verb:
1 : to receive an academic degree or diploma

If you are talking about a single student, the intransitive verb—"He will graduate in May" or "He is going to graduate in May"—is what is generally used.

Your second sentence: "He will be graduated in May," is the passive of *"X University will graduate him in May," using definition 1a (transitive). This sentence sounds strange to me because people usually use the intransitive in the active voice rather than the transitive in the passive voice (unless they have a good reason to use the transitive). However, "X University will be graduating 5,000 students in May" sounds perfectly fine. And you can come up with situations where the transitive in passive voice sounds fine with a single student, for example, "We will not be graduating Bob this year, but Ray will be graduated in May."

Definition 1b (transitive) appears in constructions like "I graduated MIT in 2009." This construction sounds informal to me, possibly because it become popular only after I learned English. I don't see any reason not to use "from MIT".

Google Ngrams shows that the transitive (1a) in passive voice was commonly formerly used for this, but is now rare, and that the popularity of (1b) is growing. However, the intransitive is generally what is currently used.

I am not going to go into the difference between going to and will in this answer; this difference has been hashed out several times on EL&U. For this sentence, both constructions are fine. The likelihood of graduation is the same for both constructions, and I consider them both acceptable in formal letters.

"To be graduated from" was formerly a common way of expressing graduation. See the Merriam-Webster entry; note definition 1b: "To be graduated from". It seems that this passive construction is always used with the preposition "from", with the object of the preposition being the school conferring the degree (for example, "he was graduated from XYZ University", or, even more archaic, "she pursued an accelerated program at XYZ University and was graduated therefrom after three years of study."

In the early 19th century, the preposition "at" seems to have been more common.

There was a time (roughly from the first to the second world war) when "he was graduated" was more common than "he graduated" (ngram), but, interestingly, there was no time when "he will be graduated" was more common than "he will graduate" (ngram).

Here is a comment by Heywood Hale Broun from Harper Dictionary of Contemporary Usage, Second Edition (1985) that illustrates the old "correct" usage, and (perhaps inadvertently) indicates how long popular usage in the United States has ignored it:

'She graduated from' is not acceptable to me. Years ago, Herbert Bayard Swope, one-time editor of the [New York] World, asked me when I had left college. 'Sir,' I replied, beginning as most people did when addressing Swope, 'I was graduated in 1940.' Although he was elderly and heavy, he dragged himself up from an easy chair and lumbered across the room with outstretched hand. 'I haven't heard it correctly used in years,' he rumbled in a voice agrowl with emotion. It was, for me, a ribbon on my diploma."

The event memorialized in this anecdote probably occurred in the early 1940s and no later than 1958, when Swope died, so it's clear that "was graduated from" has long been out of common usage in the United States.

Incidentally, the usage question that prompted Broun's response was whether the even more suspect phrase "She graduated college" was legitimate.

He will graduate in May. He is going to graduate in May. He plans to graduate in May. He is scheduled to gradate in May. In May, he will have graduated, assuming he passes all his courses. All of those are fine, and they would be suitable for a formal letter.

I graduated from Boston University. I am a Boston University graduate. I have been a Boston University graduate since 1998. Those are fine, too, but "I have been graduated from BU" is not.

As for He will be graduated in May, no, I wouldn't use that construct, not unless he had just signed up for P90X, and I was referring to the shape of his torso. Even then, I don't think he'd be graduated until the end of June at least; such transformations don't happen overnight.

_{(That third paragraph is a play on words, on the word "graduate." Please don't let it confuse you).}