Many accommodations in the islands ( Lopez Island, Orcas Island, San Juan Island ) do not allow kids because while they probably love children they understand that many guests want peace and quiet. Imagine how big of a "moment killer" the hungry little one screaming at the top of his lungs could be to a couple in the next room on their romantic San Juan honeymoon.
This page lists places in the islands that happily will accept your baby/kid/children:
http://www.desticam.com/_forums/best_family_hotel_in_san_juan_islands_with_small_children-t1565.0.htmlTry to avoid the rush hours of breakfast, lunch and dinner when eating out with children/babies so that you can get a table in an area less busy where your less likely to disturb other patrons. Another advantage to this is you get better service and sometimes a whole area to yourself for the youngsters to run amok around.
Bring your stroller along to keep your baby comfy and your back relaxed.
Bring your car on the ferry ( about $50 ) if you want to see the parks, viewpoints, remote villages and galleries. You can walk on the ferry for about $10 a person and then rent a car from here but I don't know if after the parking fees, car rental fees, and fuss if this is worth it.
Island supermarkets sell all baby supplies and there are medical centers on Orcas, Lopez, and San Jan Island.
The weather can get into the 80's in the summer months but cools down fast after sunset... dress the little guy accordingly.
Please post back to this message board with any tricks advice you learn while on your vacation.