It kind of depends on your boat and the weather. You can cross over into the gulf islands at Gabriola Passage or Active pass and then make your way down through the gulf islands and into the San Juan's. You could then clear customs in Roche or Friday Harbour if you wanted. This would be the safest route for weather. If the weather forecast is good then you can go down the Straight of Georgia and east of Orcas Islands.
Either of those routes I would go through Deception pass and avoid going on the outside of Whidbey Island as you can get big waves up the Juan De Fuca.
The straight of Georgia, in my opinion, is the worst part cause if it blows up is a long way to find shelter in any direction. In the gulf Islands you can usually get out of the wind and waves around the other side on an Island.
Check Big Wave Dave and WindAlert.com for wind forecasts and check Environment Canada for current wind readings along your route.
I did Seattle to Vancouver last June up past Everett and through Deception pass then east of Orcas Island. Was great weather and an easy trip of about 6 hours. I have a 26 foot Sea Sport.
Oh ya, watch for logs, crab traps and nets along the way!