I don't know about bagels, muffins and scones... but if you want great French-style baked goods (baguette sandwiches, kuign amann, croissants), Japanese-style bread (curry donut, anpan) and other baked gourmet creations, you will find multiple bakeries inside the Shinagawa station complex. You can't go wrong with Pompadour although they may not be open early in the morning. There is another bakery inside the Ecute section of the station (in ticketed area) which I think is open fairly early.