As one of the newest C-Brats, thanks BMC for giving me an opportunity to contribute something (hopefully) useful to the group!
I've been sailing the San Juans for a decade and keep a sailboat in Anacortes at Cap Sante Marina. If you decide to trailer up Cap Sante is a great place to launch and park your tow rig for the week.
A quick cruise through the Guemes Channel and across Rosario Strait will take you to Thatcher Pass into the San Juans (James Island just south of the pass is an excellent spot for a quick hike. It has a couple of buoys on the East side (exposed) but a dock on the West).
Just inside Thatcher Pass you'll find Spencer Spit (we find this a great place to stop and wait out any fog in Rosario Strait on our returns to Anacortes).
From there you can head for the North side of Shaw to Blind Bay (one of our favorite spots to grab a buoy or an easy anchor set and watch the ferries at night pull into Shaw and Orcas Landing). Head for the Orcas Hotel in the morning for a croissant and coffee, yummy!
Then you can head through Wasp Passage over to Deer Harbor, Jones Island, or on to Stuart, down to Roche Harbor, through Mosquito Pass over to Garrison Bay (English Camp) and/or Westcott Bay (both excellent anchorages).
I would definitely plan 1 night in Reid Harbor (many buoys, tons of anchoring room) on Stuart (hike to lighthouse is looong but fun) and either bay by English Camp or Roche Harbor. When at English Camp don't miss the short hike up English Hill for an outstanding view of the islands and Canada!
Returning from there you can hit Friday Harbor or Fisherman Bay on Lopez. Near Friday Harbor another great spot is Turn Island. Only a couple of buoys and anchoring can be tricky, but a nice hike and small spit to explore at low tide.
Going back to Anacortes you can go through Obstruction Pass (another great stop is Obstruction Pass Campground with 3 buoys off the beach) or Peavine Pass. Then over the North tip of Cypress Island and down the east side of Cypress back to Guemes Channel. On the East Side of Cypress you'll find a few good stops (Pelican Beach with a few buoys and another excellent but tough hike up to Eagle Cliff with more outstanding views), Eagle Harbor (free DNR buoys!) and Cypress Head.
On the cruising guide front, I really like "A Cruising Guide to Puget Sound" by Migael Scherer. She has great descriptions of all the good spots with excellent tips on navigational hazards nearby. I believe it's out of print now but I would be happy lend you my copy. PM me if you're interested and we'll work out a way to get it to you.
If you had more time I'd be one of the guys who says cruise up! The problem is it sounds like you only have 5 days and that only leaves 4 nights to enjoy far too many anchorages....you have some tough choices to make! Good luck!