for your tour: look into Hato Bus, they do a pretty good tour which comes with an included meal. The Panaramic Tokyo one is good, it goes to some of the spots on your list. They do pick up/drop off service too from most hotels.
as far as tokyo disney goes, its about 25mins away from tokyo in chiba and theres not too many touristy attractions around. for shopping there is an outlet mall in kaihinmakuhari that is pretty nice...but not much for kids to do.
yokohama is a cool destination but thats opposite direction from disney.