In the same area, it crosses Rausch Creek (headwater to Stony Creek). That's one valley over from Clarks.
There are also some small trout streams in Swatara State Park (I don't think the AT crosses them, but runs nearby).
I don't know if any of these spots would be awesome, but they should have water and fish in them. Also, none of them are unknown. The place where Clarks is crossed by the AT is rather heavily fished and has a huge parking lot.
Rausch Creek has a few trout in it, but for the most part, it's heavily impacted by AMD. The DFTU chapter maintains a limestone treatment well on it, but it takes time to drop the pH. So you might have to go downstream a ways before it gets decent.
I had this same idea a while back, and did enough looking into it to convince myself that it's kind of a fool's errand for the most part. Although I guess it's a great thing to say you did... the doing of it may be a bit of a disappointment though.
PS: The AT crosses the upper end of the Yellow Breeches C&R section... speaking of DISCOVERED gems! :lol: