Fly river turtles - to the best of my knowledge - are the only fully aquatic species of turtle available.
Puffer fish would surely nip at the eyes of something like that - or vice verse, in which case the turtle will get ill or die of poisoning from biting the puffer.
Either way it's a bad combo - especially with the high price on fly river turtles.
If you have your heart set on keeping a puffer - expect it to be a single fish in the tank, as all puffers are highly territorial, and will at best shred fins of tank mates.
If you have your heart set on a turtle - invest in a fly river turtle, a larger tank, and there are countless combination's of fish you can keep it with.