Believe it or not, certain daimyo employed slingmen in their armies. The actual purpose of these weapons isn't clear (that is, from a sengoku standpoint) but it has been speculated that they were intended to simply harass enemy troops and horses. The only specific reference I have seen to stonethrowing is that Takeda general Oyamada Bitchu no kami Masatatsu (d.1552) commanded a 'stone-throwing corps'.

The Kakizaki (aka Matsumae) family controlled southern Hokkaido during the sengoku period and employed Ainu (Japan's aboriginal natives) in their army. The ainu used poison-tipped blowguns and it is said that the Matsumae availed themselves of this unsual weapon in their wars to control the southern region of the island. However, no one knows how effective (if at all) these weapons were.