I have a semi-dwarf quince tree which is about 3 years old. This year it sprouted a couple of very long, thin shoots which are out of place with the tree's shape .
When is the best time to trim them back?
When the tree has ceased growing for the year. If you prune now, some new growth may emerge at the pruning point.
February at the latest, before new buds form.
I always wait until winter when all the leaves are down, making it easier to see the structure, but your 3-year old tree is probably not that complicated.