In the Tokyo Station area, I like to go to the yakatori under the tracks places. I'm happy with this as a light dinner, although to the locals (mostly salarymen) it would be considered to be more of a place to go for drinks after work.

Some major department stores have a bunch of relatively reasonable restaurants or you can just go to their food halls and buy an enormous variety of takeout items to consume in your hotel room, although I guess you could also go to a park in good weather. Tokyo Station and other major train stations have a variety of reasonable eat in and take out food outlets.