Bainbridge is more scenic due to the Seattle skyline views as you leave/arrive, plus the possibility of Mt. Rainier if it's out. The Bainbridge boats are larger and more frequent, too.

Thanks!!

You have gotten lots of good suggestions. With all the moving around and exploring (both urban and nature) - I suggest you consider a baby backpack that converts to a stroller. It has some drawbacks (baby stands uprights so hard for naps, can get heavy to carry for long periods) but we loved using it with our 16mo old in Ireland and I think she did too (I think Kelty made the one we used).