I've never had any issues eating at East Egg. Their GF pancakes aren't the greatest, but still very enjoyable. I order them often. (And I didn't have to make them!) I have not been impressed with their GF bread.
The food is okay, nothing special. Celiac people beware - they offer gluten free toast and pancakes, but the toast is thrown in the same toaster as the regular bread. Glad I asked! A small $8 investment in a separate toaster would be nice, but apparently they don't understand the seriousness of cross-contamination.
I have not tried this location yet, but have asked and they use Ener-G brand bread - alternating between brown rice or tapioca variety for their menu. They make their own blend for their pancake mix and are working on a dairy & gluten free recipe to offer soon. (I'm not sure of their CC policies with the pancakes as we have not had them yet.)
Very helpful staff!