Ninja Turtles...well they might have trouble against Logan but that's it. Perhaps gambit. But they've fought the whole race of Triceratons, Vampires, Cerberus, Grendel, and much more. Logan can be knocked out, and the turtles are alot better fighters in the comics then the cartoon, and Raph goes out of his way to kill. Sure they can't kill Logan but the others can be.
Course I have no idea what the Turtles are like in the newest mirage comics besides them being 30, Splinter dying, and Raph being bitten by a vampire, and becoming a huge, and super strong thing.
X-Men...I think Wolverine & Beast can take on any one of the turtles and win, plus Gambit is extremely agile & fast and is good at using the environment to aid him...plus its always fun to charge their weapons or thier color cordinated bandanas...Jubilee is there to blind/burn them whenever she can, take some cheap shots when she can, & wait for back up...she can dodge quite a few hits with her olympic level gymnastics...