For me, it's sort of tough between a few of them, but generally I'd go.
-1990 Live Action TMNT
-2003 Cartoon Series TMNT
-1987 Cartoon Series TMNT
Honorable Mention for Injustice 2 TMNT due to them looking very much like well animated versions of the 90's Live Action turtles. Such a great addition to the game.
90's TMNT is just too good, I love that first movie quite abit still to this day, less so the sequel and third, but I really dig how they look.
2003 was a great take on them I feel, kinda more of a design thats like a super hero show. Make them abit tougher looking, introduce more darkness into the show, overall more of a cooler look than the silly marshmallows of the late 80's.
1987 is just pure nostalgia for me. It's kinda funny to have toys of that era, where they look nothing like the show and that they never look like that until more recently they did throwback figures to the original cartoon designs. This is a silly cartoon show, but I love it.
TMNT Theme Metal
https://www.youtube.com/watch?v=AlfjNTqbFLA