Colby there are lots of choices, here are a few that you can pick and choose from. Start at Port Orchard marina, with foot ferry to Bremerton, then to Paulsbo, Kingston, Edmonds, Bell Harbor on Seattle waterfront, then Blake island, Gig Harbor, Anderson Is or Johnsons point or Boston Harbor, then Olympia, Shelton, Jarrell Cove, Allen, then 19th street or Foss waterway in Tacoma (Chahoolee glass meseum), Then Desmoins, Blake Island, and back to Port Orchard.
I would plan 2 weeks if you want to do it all or just hit the main attractions and reduce your trip time.