Do you need your car on the Island? If not, timing won't matter. Hop on the  Community Transit 417 bus from Fourth & Union (be aware this is a commuter bus and its last trip out of the city is around 6:30; otherwise, take the 511, transfer to the 113 at Lynnwood Transit Center). Each bus is conveniently scheduled to drop you off at the dock just before the ferry departs Mukilteo.

Island Transit is waiting when you get off the ferry in Clinton, is free and travels the length of the Island. Check out various routes if you need to detour off Route 520.

If you are taking your car, I would recommend waiting for the 7:00 ferry, as the majority of the Boeing workers and Seattle commuters have come and gone by then. Other than holidays and really nice summer weekends, I've not seen too much of a line after 6:00.

Get in line, pay your fare, park your car. The parking attendent can tell you if you will make the next ferry. As they depart every 30 minutes, when you get there won't make a huge difference after the evening rush hour. The parking lot holds more cars than the ferry. If there is a wait, you can stroll down to Ivar's or up to Arnie's. From either location, you can gauge the ferry's progress and finish your drink or order another.

I would think it would take longer to navigate I-5 during the evening commute, trying to get to Mukilteo at 6:00, than it would to leave the city (if taking your car) a bit later, thereby avoiding both the worse of I-5 slow-downs and a ferry line.

Hope this helps.