If my grandparent is deceased, do I refer to them as "is" or "was" my grandparent?
You would say "John was my grandfather". This is because when he died, he essentially stopped being your grandfather, so to speak. It is like if being a grandparent of parent is an occupation, like being a carpenter. You would say "John was a carpenter." Likewise, you would say "John was my grandfather."
You would use the word was because that means before, is means that they are currently your grandparents but because of their nonexistence it's not possible for them to be anything. They were once your grandparent.