Although I cannot personally recommend this tour operator by having done business with them, I had some guests recently take their Daily Afternoon Tour and they said that this is highly recommended.
They are out of Friday Harbor, San Juan Island. It was out of my own recommendation that I told them that it was a better bet to go with a tour company that was closer to Haro Strait and that means not as much sea time as an Anacortes or Port Townsend operator and more possible Whale Watching time!
If you are going for just the day, plan on it taking all day from Highland Garden House. You can park at the ferry landing west of Anacortes and walk on the ferry. The Ferry pulls right up to Friday Harbor and you walk to their office.