The music clubs achieved critical recognition after opening nearly a decade ago. Death by Audio booked shows by Future Islands, Thurston Moore and the Thee Oh Sees. Shows at Glasslands featured acts like TV on the Radio, Tame Impala and Alt-J. Both became influential incubators of talent, drawing crowds that lined up just yards from industrial ruins along the East River.

But with a shortage of commercial space in Williamsburg, even that desolate stretch began attracting new attention, including a visit by people from Vice in April, said Seth Schiesel, a co-founder of a technology start-up two floors above Death by Audio and a former New York Times staff writer and critic. Brokers working with the landlord approached him around the same time to ask about ending his lease early, which he did soon after.

Death by Audio organizers signed what they believed was a two-year lease in the summer of 2013, Mr. Conboy said, but lost their copy and were informed in July 2014 by their landlords, Sol and Leo Markowitz, that the lease ended after 17 months. Mr. Conboy said that the club agreed to leave by the end of November in return for a waiver of its last four months of rent, totaling $52,000.

A lawyer for the landlords, Ian Lester, said that his clients had waived more than $55,000 in rent payments “in an effort to amicably part ways.” He added that Glasslands had moved out at the end of December, before its lease was up. Glasslands’ owners did not respond to a request for comment.

Before the departures, the clubs and the media company had appeared to share a sensibility. Last year Vice’s music blog, Noisey, offered a $235 spring season pass to Glasslands as a contest prize, writing, “Nothing pleases us more than getting sweaty and dancing around at Glasslands.” In 2013 Noisey described Death by Audio as “pretty much the best and weirdest DIY venue in Brooklyn.”

“When I first heard that they were the ones moving in, I naïvely rejoiced,” Mr. Conboy said. But as contractors for Vice began working loudly in parts of the building, and patrons argued about reasons for the club’s demise, Mr. Conboy said he felt as if the company were “driving a wedge inside parts of my life, my community, my friends.”