Pretty sure liveaboards are allowed at the Port Orchard Marina (Port of Bremerton), Bremerton Marina (also Port of Bremerton), Sinclair Inlet Marina (private), and Port Orchard Railway Marina (private).
We have our boat moored at the Port Orchard Marina and so far have been pretty happy, though we've only been there for a few months now. Both the Port Orchard Marina and the Bremerton Marina seem to have pretty nice facilities. Laundry
facilities on site and free showers in the tenant-only restrooms (that are kept very clean).
The Sinclair inlet marina didn't seem too bad when we were looking, but I'm not sure they have slips for a 42'er. The PO Railway Marina doesn't appear to have anyone on site anymore for operations, I know their billing now goes through a lawfirm out of CA I think.
I think Port Orchard is one of the least expensive places for moorage in the sound, so that's nice. Gig harbor is definitely a fancier setting, but is also more expensive. PO and Bremerton offer easy access to downtown Seattle
via the ferry
system, the Seattle ferry
leaves directly next to the Bremerton Marina, and there's a foot ferry from the Port Orchard Marina to the ferry terminal next to the Bremerton Marina.