I go to Angel Seafoods on Grant St & Clark Dr. They are a restaurant supplier, but they do have a retail store if you go in the front door. They do have fresh wasabi sometimes, but you'll have to ask for it. I'm not even sure they'll sell it to you if you're not a restaurant. I can because as an ex-chef I still know everyone there, and they still sell me anything I want at restaurant prices.
The Asian store at the Granville Island Public Market sells fresh wasabi.