If you're just passing through it's not a big deal. It can get unruly on weekends as has been noted. The main ship channel on the US side is the best bet and you can reenter the small craft channel a little farther west. Passing under the Ivy Lea bridge on a busy Saturday afternoon in late July can be a challenge. I recommend avoiding it if possible. We've seen 50' houseboats goin' full bore ahead and loosing ground! :-)
Watch out for the triple decker tour boats. They toss a mean wake and don't slow down for anybody!
The absolute best time to tour the islands by water
is early fall. You'll have the whole place virtually to yourself.