Fresh(raw) wasabi(生わさび nama-wasabi) is not long life.
Departments food floor in Shinjuku and other area sales sometimes
but ask store staff of regular super market before.
Say "Tube type ja nai nama no wasabi oitemasuka?"
(チューブタイプじゃない 生[なま]のわさび 置[お]いてますか？)
And last weekend 26 Oct in Ginza[銀座] opened new "antenna shop" of Nagano,PF.http://www.ginza-nagano.jp/access
Nagano,PF is one of soba and wasabi famuos area
dont know sales(in stock) or not but asking worthful maybe.
Good wasabi needs good clean stream in deep mountain side most.
Okutama,Tokyo west area,too. A day trip Okutama[奥多摩] very easy
by JR Chuo and JR Ome[青梅] line trains from Tokyo[東京] or Shinjuku[新宿] stn.http://www.town.okutama.tokyo.jp/kankou/acsess/access-t.gif
Hachioji[八王子] Haijima [拝島] (suica/PASMO valid until Okutama)
But Okutama area wasabi field(farm)[わさび田 wasabi-da] are
access very inconveient from station and not open for tourist usual.
If want to visit ask sales store staff or Soba restaurant owner.
Best wasabi season starts soon.
New Soba[新そば shin-soba] season starts already.