Just thought I'd also mention this, even though I've not been (didn't know such place existed). I just found this via Google.
Inside Atre at Shinagawa Station, there is a new gourmet food section called Food & Time Isetan. Inside that, there is apparently an area called "Food Court & Deli" featuring six shops including bakery, deli, salad bar, taqueria. They open at 8am (10am on Sa/Su/holidays).