Groceries and other supplies will be more expensive in the Islands, so if you can stock up on most of what you'll need in Anacortes, Bellingham, or wherever you intend to launch, you will find better prices and more options. Friday Harbor has 2 decent grocery stores and a couple boat stuff places (West Marine, King's Marine, Friday Harbor Marine), as well as a great variety of restaurants.
We generally get our basics where the price and selection are the best, then buy fresh produce, meat, and bakery items along the way.
Just for conversation sake, Pender Harbor (Harbour) in on the mainland in BC, quite a ways north of the San Juans. Bring your passport. With two weeks to spend in the San Juan Islands, you will likely want to see some of the Canadian Gulf Islands, too. Bedwell Harbour is on South Pender Island, in the Gulf Islands... just a few miles north of Stuart Island (part of the San Juans). Poet's Cove at Bedwell is a fun overnight - great hot tub and swimming pool. Victoria, on Vancouver Island is also a great stop, especially if you can get dock space in the Inner Harbour.
If you decide not to go into Canada, there is plenty to keep you entertained in the San Juans. One of our favorite places in the San Juans is Stuart Island - no marina there, but there are mooring balls, decent anchoring, and very limited dock space. Great hiking and fun surprise at "the Treasure Chest."
We are living on our boat this summer in Friday Harbor, working for a whale watch company again. Drop me a note if you want any other local information.
Best wishes,
Jim B.