(covers information from several alternate timelines)
A cargo container was a container for the storage of cargo.
In 2374, as part of a bribe to keep Quark from pressing charges against Grathon Tolar, Captain Benjamin Sisko agreed to get Deep Space 9 station security to release several cargo containers that they had been holding due to his not having the proper import license. (DS9: "In the Pale Moonlight")
That same year, during one version of the alternate timeline known as the "Year of Hell," a Zahl Ambassador threatened to send a Krenim Commandant home in a cargo container and seize his vessel if he didn't leave Zahl space. (VOY: "Year of Hell")
In 2375, when Prax materialized transporter patterns for what he believed to be more than a dozen telepaths on the USS Voyager, he ended up with cargo containers filled with vegetables instead. (VOY: "Counterpoint")
In 2376, Icheb threatened to place Azan, Mezoti and Rebi in a cargo container and send them back to the Borg if they didn't stop asking him questions about his family and what would happen if he left Voyager. (VOY: "Child's Play")