The best source of information on hoikuens and kindergartens is your Daily Living Guide for Foreigners given out by your shiakusho or kuyakusho (city or ward office), for e.g., the local ward office in Yokohama gives out “Daily Living Guide For Foreign Residents of Yokohama” which contains the phone numbers and locations of daycare centers, preschools and kindergartens in each ward. You can try the Prefectural homepages as the guides are usually accessible online too.
Japan Hoikuen Association (In Japanese)
Contact these websites for information and listings of hoikuens in Japan: Kids Information Service and Zenkoku HouikuRenrakukai 全国保育園保健師看護師連絡会 (both websites in Japanese only)
For a April-March year-long account of Daily Life at Japanese Public Daycare by Cornelia Kurtz