I would recommend staying close to Seattle if that is where you are chartering. The San Juans are 8-10 hours away. That's a long slog up and back. A long day each way. Not much to do along the way either. And the journey would be weather dependent. Motoring up there is very different from river cruising.
There are plenty of great destinations closer to Seattle that would offer shorter trips and more opportunities for relaxation and exploring. Eagle Harbor and Port Madison on Bainbridge Island, Blake Island, Gig Harbor, Poulsbo, downtown Seattle, Port Ludlow, etc. All are just a short hop from each other. Port Townsend would be great, but that is 5-6 hours north. I wouldn't go farther than that.