Here is a book I would highly recommend...
A Cruising Guide to Puget Sound and the San Juan Islands
LINK
We have used this a lot in the sound and a bit in the San Juan islands. Worth every penny, and I tend to be rather frugal. Great information about all the little places, where you can get ashore or not, hazards that may be around anywhere you might want to anchor, etc.
Another good resource is...
Gunkholing in the San Juan Islands
Amazon.com: Used and New: Gunkholing in the San Juan Islands
... and is likely available from your local library if you live in the pacific northwest.