There is a reference to the 1979 movie, The Warriors, when Bebop says, "Turtles, come out and play."
During the battle, April's hair stands up and she hurls chunks of concrete at Shredder via her telekinetic powers. This is a reference to Tetsuo from the 1988 movie, Akira.
During the Chris Bradford cartoon the group is watching at the beginning, the character Lil Rineo transforms into a giant yellow skinned monster with a Mohawk and metal arm. This was the mutated look of the character Carter, who joined the turtles in season 9 of Teenage Mutant Ninja Turtles (1987).