Furusato mura should be added to your choice.
It is center of the tourist place in Niigata as it doesn't only have tourist information center and souvenior shop but also offer the tourists events related to Niigata almost everyday.
It also have the free indoor equipment for children. It's not so big but good enough to satisfying children's boredom in rainy days.
NIIGATA FURUSATO Mura VILLAGE
2307 Yamada, Nishi-ku, Niigata-shi, Niigata Prefecture 950-1101
OFFICAL SITE(English) : http://furusatomura.pref.niigata.jp/eng/