I personally like Coron better than Puerto Princesa, but Coron is more for snorkeling and diving, so might not be appropriate for most kids. Depends if they're comfortable swimming in the ocean or not.
I've never been to both. But as a rule of thumb when travelling with kids, always bear in mind the location with hospitals. I'm guessing Puerto Princesa is more accessible to hospitals.
One of my consideration as well when travelling with kids is the proximity of the hospitals in case of emergency. With that, my vote goes to Puerto Princesa.
For me Coron is the best , its one of the best beaches in the world . Puerto princesa is also beautiful but its bit common already .