We use Prime Travel for your trip to Hokkaido and love it!
The company's boss is Japanese and the guide is a local Japanese.
Prices are little more than that offered by local travel agencies but it is worth it.
Accommodation included 5* resorts as well as ryokans. Meals are Japanese, if you do not eat sashimi, they can prepare cooked food for you if you let them know. They also allocate enought time for sight-seeing and shopping.
We have since recommended to serveral friends and all they all love it.
Their website is
http://www.primetravel.com.sg/fmj.asp.