Ooh, I know this one! I'm a Freemason myself and after getting asked about this a few times, I read up on it. William Morgan was, to be quite clear, a generally unpleasant man, and a failed businessman. Depending on your sources, either despite this, he somehow managed to join a Freemason's lodge in Batavia, in upstate New York, where he lived at the time, or he deceived actual Masons into thinking he was a Mason and gained entry into a lodge and witnessed some ritual.

In September, 1826, he announced that he was going to publish an exposé of Freemasonry, containing all its "secrets." Given that he personally was never raised to the degree of Master Mason, his exposé would actually have been laughably incomplete.

Regardless of this, several local Freemasons decided this was unacceptable, and kidnapped him (after allegedly - and probably - setting fire to the printing office of David Miller, Morgan's publisher) as he left a jail he'd been imprisoned in for debt. The conspirators claimed that they took him to the Canadian border, gave him $500, and told him to never show his face in New York again. However, it is entirely possible that they simply drowned him.

In conclusion: yes, it is pretty much certain that Masons, as individuals, were behind his disappearance. We unfortunately cannot rely on court records to provide us with any solid evidence: twenty six men were indicted, and of these six were tried, none on murder charges. It transpired that the prosecutor and many of the jurors were Freemasons, and the trial resulted in very lenient sentences.

Sources: Andrew Burt, American Hysteria, 2015; John Hamill, The Craft, 1986; Christopher Hodapp, Freemasonry for Dummies, 2013.

As a postscript: I find it hard to believe that the perpetrators attacked Morgan purely because he claimed he would expose masonic secrets: there have been dozens of such publications long before Morgan came on the scene, and given his generally terrible reputation it seems likely to me that this was probably simply the straw that broke the camel's back. Regardless of this, the perpetrators were in clear violation of their vows, and acted in an incredibly unmasonic manner - to this day, especially in the US, the Morgan Affair is cause for some embarrassment, although it is the only reported case in history where someone was attacked in such a way for threatening to reveal "secrets."

This also seems like a good time to plug /r/freemasonry, which is a fantastic community full of people who can probably answer this and other questions you have far better than myself.

While it is impossible to say for sure what happened, the most likely scenario seems to be that people associated with the Freemasons were involved in his disappearance in some way. Most professionals I know would probably point to the Freemasons as responsible to various degrees, but how much of it was officially endorsed by higher ranking officials within the Freemasons is unknown. It is entirely possible that the official line was only to harass him into dropping his book (which was not necessarily illegal at the time), but a few lower ranking members decided to kill him. Or maybe he was kidnapped to be beaten or left in Canada to wander home as a message and he died in the wilderness. Or maybe they had nothing to do with it at all. We will likely never know. While people in the Freemasons would be complicit or guilty for his death in some these circumstances, it is difficult to say THE Freemasons, all the way up to President Jackson, are responsible for his disappearance and death as people in the Anti-Mason party would have wanted you to believe. People often love to see a vast conspiracy where only coincidences exist.

From what little is known, there are an awful lot of circumstantial occurrences that all tie back to the Freemasons. Shortly after Morgan announced his book's coming the harassment began from people associated with the Freemasons. Newspaper clippings denouncing him, sudden unpaid debts being called in, and his arrest and disappearance are all conveniently timed. Several people who were members of a Masonic lodge admitted to kidnapping, but not killing Morgan. One person reportedly even confessed to the murder on his deathbed. The fact that several Freemason people were found guilty of crimes related to his disappearance should lend some credence to the theory; however, you should also weigh political motivations for the convictions.

The most important takeaway is that many American people believed that the Freemasons killed Morgan to keep him quiet, regardless of the Freemasons actual guilt. The Freemasons were growing into an elite organization that reeked of nobility and anti-republicanism to Americans of the early republic. To your average American, it appeared that nearly every powerful politician or judge was a Mason. Nearly every judge, magistrate, sheriff, and jury involved in the Morgan affair was packed with men associated with Freemasons. Whether they were a part of a massive conspiracy or not is impossible to say, since it would have been difficult to find a judge who was not a Freemason at the time. Some people genuinely believed that Masons were in control of the United States, while others joined the movement and co-opted Morgan's disappearance as a way to further their political career.

Sources: What Hath God Wrought: The Transformation of America, 1815-1848

A Shopkeeper's Millennium: Society and Revivals in Rochester, New York, 1815-1837

Horace Greeley: Champion of American Freedom

The above three books are by some of the best historians and off the top of my head discuss the Morgan Affair and the atmosphere surrounding it. None of them stick their neck out to conclusively blame the Freemasons, though they do note that it would be an extreme coincidence if some Freemasons were not responsible.

Edit/Addendum: In response to some of the other replies, I don't think comparing the Freemasons of the 1830's to the Freemasons today works on many levels. Not only were the politics, ethics, and leadership of the two time periods very different, but the Freemasons of the early republic are a vastly different group with very different motivations than the Masons today. Saying that their actions appear un-Masonic or against the spirit of Freemasonry as we interpret it today is a misstep. For example, despite being founded on ideals of liberty and equality, few Freemason lodge in the 1830's would have accepted a black applicant. (A few Prince Hall lodges existed which have been retroactively endorsed, and there were a few extremely rare cases of black members in the United States.) This does not mean that all Masons in the 1830's went against the teachings of the Freemasons, only that we now see the world differently.