For lodging in Anacortes, we recommend Airbnbs or Vrbos. There are also a few hotels in Anacortes but they are all local small hotels. Whether you book a hotel or an Airbnb / Vrbo, we recommend booking well in advance since June is prime tourist season in Anacortes and the San Juan Islands.
Mount Vernon and Burlington are a 30-minute drive away and have more options for hotels (Marriott, Hilton).
La Conner is a cute tourist town that is about 20 minutes away, but definitely book well in advance if you want to stay here.
The drive from Seatac Airport is about 2 hours on I-5 North.
If you're flying into Paine Field in Everett, the drive is about 1 hour on I-5 North.
To get here from Kitsap County, the best way is to take the Port Townsend / Coupeville Ferry. To guarantee a spot on this ferry, make a reservation on the WSDOT website to get there and for the return trip. This trip takes about 3 hours.
Another option is to drive around through Tacoma and onto I-5 North. This option takes 3 hours with minimal traffic.
Last option is to take the Kingston / Edmonds ferry and drive up to Anacortes on I-5 North. However, this ferry does not take reservations and I-5 North can get very busy so this trip could take 3 hours or more.