I can only speak from my experience and knowlegdge, I suspect I used to live in the same area as you but if not perhaps my thoughts might help anyway.
I for a time lived in Bremerton WA which is about a 1 hour ferry ride from Downtown Seattle. The boat ride is about 1 hour. So here are some tips and tricks from someone who rode the ferries on occasion and someone that knew people that did all the time
1) Riding a motorcycle/moped/bicycle/walking on is FAR FAR preferred to driving on. The wait times for cars on the way back are really crazy. Don't expect to show up with your car at 4:00 to be able to get on the 4:20 boat. You will be waiting for the 5:30, or even 6:30. With the other modes of transportation, you skip the queue. As long as you show up around 4:15, you're good.
2) The ferry schedules are not such that one leaves every 5 minutes, one leaves every 90 minutes. How much control do you have over your work schedule? Do you know with certainty that you'll catch the boat you want to catch at least 98% of the time? Missing the boat SUCKS.... Take your 1:45 one way commute and add 1:30 to it... that is the cost of delay. If it's going to happen more than once a month, it would be enough to put me off of this commute. Also, how much patience do you have for ferry break downs, or ferries being late, and would your employer be OK with them? I don't know how common they are nowadays, but it felt like once a month there was always some kind of problem.
3) In favor of the ferry commute, some people really turn it into productive time. There are massive lines of power plug ins in the girls' bathroom, you see people doing their hair and makeup there all the time. Take a shower, get on the boat with your wet hair and do it there. People read/work on the net, etc all the time. You also see people doing laps on the boat, getting in their daily exercise. The walk ons, if they are early, scope out the bench seats and take naps.
That said, I changed my 30 minute commute to a 70 minute one and I'm exploring going carless. For me, I enjoy reading blogs and books so I just do it on the bus now rather than at home. I never was too productive in that extra 40 minutes at home and so the longer commute to me is worth it, if I can ditch my car. Of course if you're tied to having a car, the extra $3 in gas it cost me a day wasn't a big deal really, it's being able to ditch the maintenance/insurance that really make it attractive.
Hope this helps.