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The Turtle Copter is one of the main sources of transportation of the Turtles in the Back To The Sewer season.
It is likely this is the same mode of transportation used in Season 4. If so, it was introduced in "Insane in the Membrane" as one of Agent Bishop's helicopters that Stockman used to fly to New York City. It was commandeered by the Turtles when they were chasing Stockman, and they kept it at the end of the episode.
It was revealed that Donatello was modifying it throughout the outbreak and the Turtles used in the Good Genes episodes to travel to Area 51.