Shouldn't be a problem at the Fujiya Hotel - they've actually marketed themselves at foreigners who want to get married/honeymoon in Japan. The link I wanted to post from 2005 is dead now. It included this:
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Share the Same Memories as World Celebrities

Fujiya Hotel started business in 1879 as the first full scale international resort hotel in Japan.
It has been loved by many celebrities including Charles Chaplin, Helen Keller, John Lennon & Yoko Ono, and the Japanese Imperial Family.

After a Japanese-style wedding held at Hakone Shrine, which boasts a history of over 1200 years, enjoy staying in the Flower Palace, well known among distinguished foreign guests, and a dinner in the main dinning room The Fujiya. The ceiling of the dining room is painted with flowers, butterflies and wild birds in a motif of nature's bounty in Hakone. The beautiful space will be the perfect setting to celebrate your new relationship.

*The hotel offers both Japanese and Western-style weddings.
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There are costs for some of their set 'plans' here: http://www.fujiyahotel.co.jp/fujiya/...an.html#enishi

Costs for sample menus here.

I hope at least this helps when you're making comparisons.

(The Ukai Toriyama is a restaurant housed in a collection of 'private' buildings and is less than an hour from Shinjuku - I suggested it as it would have been my own 'fantasy' venue if I'd have married in Tokyo).