Well, since nobody seems to know I found some more destinations if anybody is looking and stumbles across this later:
AXIS Building (AXIS Gallery, Japan Industrial Designer’s Association Design Museum, lots of ID related shops): AXIS Inc.
Map here: http://www.axisinc.co.jp/access.html
Droog Shop + Showroom: http://droogdesign.jp/droogshop.html
KDDI Designing Studio (keitais / cell phones): http://www.kds.kddi.com/access/
Panasonic Center (Gallery, ECO/Universal/Math+Nature Design exhibitions, ECO house): http://www.panasonic.net/center/tokyo/access/index.html
With the exception of Panasonic, which has exhibitions on the design process and concepts, seems like most big Japanese electronic companies have their own showrooms oriented to the everyday consumer.
JVC/Victor Showroom: ご指定いただいたページが見つかりません。(404 Not Found) | JVC
Sharp Ichigaya (Tech + History showrooms): シャープミュージアム
Sony Building: http://www.sonybuilding.jp/e/index.html