Both are big enough to boat down. I'm pretty sure they'd be deemed navigable.
They probably are navigable, but whether or not you can float a canoe has pretty much nothing to do with it.
It's about commerce. Meaning, barges. And while the test is whether it is capable of, since water commerce isn't as common as it used to be, the courts have generally been interested in whether there is evidence that it WAS used for commerce. Way back then water was the primary means of transporting stuff, and it's why many towns are on waterways. If it has a town on it, it's likely navigable.
So if you have some historical documents showing barges going up and down. Or a towpath/canal type system. Maybe an old grist mill which transported it's product down to town by boat. That's the kind of thing they look for.
In the case of Penns, I think it'd be pretty open and shut. Many of it's landmarks were named by those who used it for "commerce". Butter Rocks, for instance, is where a barge of butter crashed. The Spinning Wheel was an area for barges to avoid or else they'd get caught there, with their water wheel spinning but not moving the boat! Coburn was a jumping off point through the mountains, a port, with Millheim being the rest stop on the other end.
Some history can be found here:
http://www.unioncountyhistoricalsociety.org/OnceUpon/Article24.pdf
Yet, Donny Beaver has his posted signs up there anyway, without challenge.
As for the Salmon River, again, that's in NY. While this is based on Federal Law, it's pretty much up to the states on how they determine navigability, and what rights are attached.
The East Branch, well, I'd guess based on location and size that yes, it's navigable, and that you'd be able to find plenty of evidence in support of that. But you'd have to put in some research time most likely.