Some fascinating responses and stories - thanks.
I started this thread with the expectation that more of the west side folks would chime in. After all, this is where they are native and common in creeks (like Connoquennessing as greenghost points out above). Pretty much any un-dammed mid-sized creek in western PA should potentially hold some muskies if the habitat is suitable.
Nevertheless, I have never seen a muskie up in a small "trout stream" sized creek with any degree of elevation.
jifigz,
I think it highly likely that there is some limited, natural repro in the Juniata. Perhaps with the evolving musky management plan, such evidence will come to light. Next time you're out in the springtime, keep an eye out for pairs of adult muskies cruising the shorelines. I have seen this in other waters and it is indicative of spawning activity (if not success).