The ferry ride with the best views of the mountains and the Seattle skyline also happens to be the most convenient for most tourists: the Seattle to Bainbridge Island route- with the Seattle to Bremerton route as a close second place. Both leave from the Downtown Seattle Ferry Terminal. I recommend the Bremerton route if you just want a ferry joyride- it's about 50 minutes each way. Take the Bainbridge route (30 minutes each way) if you want to spend some time on a PNW island; Bainbridge Island is pedestrian-friendly and has lots of things to do.