I don't remember a Choo Choo Pizza, but I do remember Royal Line Pizza. I'm not sure it's what you're describing though. Royal Line had a glass-enclosed train that ran parallel to the tables, and the train with your order would stop at your table, and you opened up the door to get your food. I remember the pizza being thin cracker crust, which I never get, but I thought theirs was delicious! And I always had fun playing Sega Sonic the Hedgehog tableside.
I may need to visit Pizza King sometime for the nostalgia! Never been there because it's across the magical river that's apparently too hard to cross!