General:
* Small
* Tiny
* Little
* Minute
* Diminutive
* Weak
* Frail
* Feeble
* Insignificant
* Unimportant
More informal:
* Scrawny
* Skinny
* Undersized
* Wasted
More formal/literary:
* Paltry
* Meagre
* Trifling
* Inconsiderable
The best synonym for "puny" will depend on the specific context in which you are using it.