There are actually four. Twice the number of Bubbys in America!

http://www.bubbys.com/our-restaurants/japan/
http://bubbys.jp/

I think the Yaechika one has the best lunch menu, but you can't go wrong with any of them.

Another good place for pie is Anna Miller's, just across the street from Shinagawa station.

http://www.bento.com/rev/1404.html

There used to be over a dozen in Japan (the main branch is in Hawaii), but this is now the last one standing.