Mario is a plumber who has somehow found himself in a land of magic stars, giant evil turtle like creatures and moving plants that give him special powers.
Any one of the Ninja Turtles are a highly trained stealth fighter with a specialized weapon.
Pro’s and Con’s
Mario can jump, fly after a run, and shoot fireballs among other things. But all of his individual powers are limited in their uses. If he wants to fly, he needs a good running start. While flying is isn’t very nimble. If he is using the his cape, or raccoon tail to hit the Ninja Turtle he has to do a good job in timing it, because of how short both items are. Fireballs can only be fired so fast, power stars have a time limit.
The Ninja Turtle has spent years in training. Learning the in’s and outs of martal arts. The only major disadvantage would be a limiting shell.
The Ninja Turtle would win. Yes, Mario has a dozen different powers to choose from. The problem is they all have limitations easily exploited by a trained fighter. The only real concerns for the Turtle would be the power star or fire flower. Mario does move slightly faster with the star, but its doubtful that it would be fast enough to catch a Ninja Turtle. All the Turtle needs to do is stay away long enough for it to wear off. The fire flower is to slow to be effective. Mario also can use his metal form, but again, it wears off. Added to that, it makes Mario much slower.