I'm with CaptKermie. Thru the islands is faster, maybe more scenic and definitely has the benefit of having a lot of places to stop (Parks Bay on Shaw Island across the channel from Friday Harbor is really nice for example). Downside, like everwhere else if there's no wind, one motors.
Over the top of the San Juans is great sailing and Sucia is the jewel. We do not like the crowds in Fossil Bay and Echo Bay prefering Fox Cove (only 4 mooring balls, no other room, beautiful sunsets) or Shallow Bay (which feels like one is moored in the channel).
Either way, find/buy the current atlas for the area. Big miles in the San Juans are only possible with a favorable current AND winds.