Throughout the show, it's been said that the turtles have had 15 years of ninja training. Leonardo also mentioned that there's been 15 years of training in Future Shellshock. Then when the turtles find out they're in 2105, Raphael said they're 100 years in the future.
Considering all this, there's no way The Shredder Strikes takes place in the 90's. I would say it takes place in 2003 at the earliest.
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