You won't get any looks because Japanese people are too polite, but it is still considered rude to walk around and eat. I bet if you had something messy like ice cream they wouldnt let you in the queue until you finish, but a popcorn bucket would be fine. Also no eating or drinking on the train unless it is a longer one like a shinkansan.
And don't ever put shoes on seats. People will give you a dirty look and might say something. That's a much bigger faux pas.
I"ve heard its culturally unacceptable to eat while you"re walking around; what about standing in line for an attraction?
...We ate our popcorn in line but when we were getting closer to the front an attendant would ask if we had popcorn in it so she could tape it shut before we rode.