I have been searching some good provider who provide both data and call service for short term visitors to Japan.
Seems most of the providers provide only data service.
After more search come across http://www.globaladvancedcomm.com/index.html
This company have rental phone (includes sim) service, Rental SIM card service for your existing phone, Rental data card service, Rental pocket wifi service
As per my research renting phone is economical. An Iphone 5 will cost 14,200 for 21 days Refer http://www.globaladvancedcomm.com/iphonerent.html for rate details
Renting SIM alone is a little expensive (for example around 21,000 for 21 days) Refer http://www.globaladvancedcomm.com/simrent.html
Both options : Renting phone or Renting SIM comes with data and call service. It includes 1,000 JPY worth call for free and unlimited data. You can charge the SIM using your credit card for additional call service.
Hope this information is useful for some of you !!
Other reference sites ..Useful for data only services
https://www.sakuramobile.jp/
http://www.so-net.ne.jp/prepaid/en/index.html#news
http://service.ocn.ne.jp/mobile/one/visitor/en/product/