Sorry for missing this question George... for anyone in the future looking for transportation out to Stuart Island there are a few different water taxis offering the service departing from San Juan Island , Lopez Island, and Orcas Island. There is no schedule and the water taxis and they are private hourly charters. Here are a couple companies serving Stuart Island:

http://www.outerislandx.com/ Up to six peole for $150 each way. "Pick-up and drop off is also available from Lummi Island, Anacortes, Bellingham, Vancouver, and Victoria. We will pick you up anywhere and take you anywhere."

http://www.sanjuansafaris.com/ Serves Stuart: $250 per hour

http://www.sjiwatertaxi.net/ No prices on their site but they take credit cards!

More info here: http://www.google.com/search?hl=en&q=stuart+island+water+taxi