You have both hills and urban areas blocking about the whole east side of San Francisco Bay. Hard for me to imagine being able to get through that. And further north you've got the Central Valley.
It really depends on the watersheds. You can get to Boston from pretty far north but you would have to cheat by going down the coast from the mouth of the Merrimack River which I think captures all the rivers in southern NH/northern MA.
Regarding Boston, the interesting thing is that it used to be connected to the Merrimack via the Middlesex Canal. My understanding is that this is silted up now (which you presumably already know) but it shows how many more connections we used to have.
Not sure you can do the equivalent further south but it looks like you could do a lot of it that way--at least in theory.