(covers information from several alternate timelines)
A cargo container was a container for the storage of cargo.
In 2151, a shipment of cargo containers were beamed aboard the NX-class starship Enterprise while Tactical Officer Lieutenant Malcolm Reed and Travis Mayweather, who was now serving as a helmsman and ensign on Enterprise, stood nearby and conversed about the ship's transporter, shortly before the vessel's launch. At least two of the cargo containers were carried out of the transporter alcove by junior officers. When Reed opened a third case, he was frustrated and disappointed to find Starfleet had sent him a load of valve sealant, when he had actually requested plasma coils instead. (ENT: "Broken Bow")
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 official 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")