Cafe Zaiya (more like a Japanese deli): I've been a loyal customer of Cafe Zaiya's since I moved to New York from Japan 4 years ago. Their midtown location (E. 41st St btw Madison and Fifth Avenues) is the best and biggest.
http://www.zaiyany.com/
Panya Bakery
http://www.yelp.com/biz/panya-bakery-new-york
Takahachi Bakery
http://www.yelp.com/biz/takahachi-bakery-manhattan
Cha-An Teahouse: I go there often.
http://174.132.150.226/~sobayany/ct/site/index.html
ChikaLicious: You can enjoy their dessert course! Chika-san's desserts are amazing.
http://www.chikalicious.com/
Minamoto Kitchoan
http://www.kitchoan.com/E/index_b_natsu2004_e.html
http://www.zaiyany.com/
Panya Bakery
http://www.yelp.com/biz/panya-bakery-new-york
Takahachi Bakery
http://www.yelp.com/biz/takahachi-bakery-manhattan
Cha-An Teahouse: I go there often.
http://174.132.150.226/~sobayany/ct/site/index.html
ChikaLicious: You can enjoy their dessert course! Chika-san's desserts are amazing.
http://www.chikalicious.com/
Minamoto Kitchoan
http://www.kitchoan.com/E/index_b_natsu2004_e.html