The thing about the Ninja Turtles is... how would they get sealed in the first place? Simply put, the Ninja Turtles simply
do not compare with the Naruto ninjas on any level. I can't see any way for them to do something
worth getting themselves sealed.
Physically? No comparison... Naruto ninjas would pound them into the ground, without breaking a sweat.
Techniques? Also no comparison... Naruto ninjas have
far more options available to them.
Skill-wise? The Ninja Turtles may be superior in skill when compared to other ninjas, and the like,
in their own reality... but they're also limited to more mundane skills and physical abilities. Naruto ninjas have no such limitations.
Mindset? Again, no comparison... Naruto ninjas are willing to kill and/or do grievous harm, if necessary. The Ninja Turtles avoid doing even permanent injury, let alone killing... to the point that
they end up captured and/or injured in the process.
When your enemy is willing to maim/kill you, and you are
unwilling to do the same... the only way to avoid injury or death is to be superior enough in skill and/or physical ability that he can't hope to touch you.
Even if they could get the skills and abilities necessary to be a threat, which
is a possibility with some time in Naruto's reality, their mindset would still pretty much kill the idea outright.
They're not going to go tearing through Konoha, killing people... and I can't see the Yondaime giving up his life to seal someone who
isn't a threat to the survival of his people. He'd be more apt to simply kill them and be done with it.
For the idea of the Ninja Turtles, you'd have to find some workaround for those problems.
Maybe they were hit by a dimensional bomb and bounced to Naruto's dimension, destroying a noticeable portion of Konoha. Then they were attacked, for obvious reasons, and they managed to
not die. Once away from Konoha, they started searching for a way home.
During that time they picked up some ninjutsu, taijutsu, and genjutsu skills, while Donatello worked on their way back. Finally, he completes it... but it would require them to go back to Konoha.
When they go back, they start the transdimensional generator and then
it explodes spectacularly... possibly due to a dimensional shield, conflicting dimensional energies, or a Konoha ninja spotting them and damaging the generator. When it exploded, they were obviously attacked.
So that was twice part of Konoha was destroyed, along with the people in it, and the Ninja Turtles were at the center of the event. And thanks to their new skills, they're far more able to hold their own when they're attacked this time. The Yondaime, with the opinion that he could
not allow them the chance to get away and come back to kill more of his people, decides to end their threat once and for all... he seals them.
And... that's that.
--
New Suggestion --
A couple things I don't think has been suggested yet, but can't remember for sure...
Tarrasque. A Naruto who can shrug off most weak to mid-powered taijutsu, almost
all ninjutsu and probably genjutsu, and regenerates what damage
does slip by. And all he has to do to keep his 'visitor' happy is eat like Chouji.
Zeus, Raiden, or Thor. A Naruto who regenerates, has godlike physical abilities, and an affinity for lightning that surpasses anything Kakashi or Sasuke could ever
hope to match.
And that's not even considering the other things they're notable for.