One thing I've learned about river fishing is there are certain spots fish will hold or stage usually year after year. There is also a lot of dead water that just doesn't hold fish , so a lot comes with trial and error or experience. I personally like slower tail out water before a strong riffle if that can be found. Feeder creek mouths also seem to hold fish steady too, and yes they prefer the main river current mostly. I think a lot has to do with oxygen and temps of the feeder creeks and I'm sure some bait washing in also. 
 
I'll see Pike move up into these small feeder creeks a lot during spring spawning in March.  

I have heard / read that hair jigs produce in the colder water.  I have been trying hair jigs and I got to tell ya,  I haven't got a bite on these things.   How am I to fish these?  Just real them in? Suspend them vertically?  I usually fish them when the bite gets slow and don't give them much time.  I have no confidence in them.  I feel like I'm wasting my time using them.  Anyone out there have any pointers for me? 

Get yourself a bucket of creek bait. Shiners, Chubs maybe even some Suckers. 3 to 4 inches.

https://www.youtube.com/watch?v=BKTZ6kV8fio

Can't argue the live bait thingy.

I am however an avid fan of jigs. But first and foremost a firm believer that it is a must, an angler have faith in his bait live or not.

Second it is important that an angler understand his quarry.

Third an angler must have faith that his quarry exist in the area where he chooses to fish.

Fourth, an angler must have faith in his presentation, given his quarry.

If your looking to go "catching" fish in numbers and or bragging rights, your number one game plan is to fish pre-spawn conditions for your quarry.

If your looking to enjoy the outdoors and build fond memories along with catching a fish or two than your looking to go fishing.

Anyways, pending your quarry, jig size does matter given this time of year. But more importantly, the colder the water the slower your retrieve of your bait. As a wise Ole angler once said, if you think your retrieving too slow, than you need slow down.

Jigs are fun and can be presented in multiple ways but it is very necessary to keep a taught line the entire time the jig is sinking. Most strikes will occur as the bait sinks. Hopping your jig back or dragging the jig until you bump then hop the jig over the object can be deadly. Just remember, the colder the water, SLOW DOWN.

Try different retrieves but always slow.

I find, say for Crappy, a jig with few hairs an inch or two works good for me. While jigs tied heavy with 1" or less hair works good for smallies in the criks and rivers.

Large mouth like the longer thicker haired jigs when ya bump a sunken log or throw into a pile of wood. Use heavy thicker hair to serve as a weed guard at the hook and thinner longer hairs to represent your bait. Just don't overkill with the hair.

Always remember to have faith in your fishing cause guaranteed, something good will occur, giving you some great memories.

OH....and if you do not catch something, there's always a good reason....... stupid fish!!!

Tight lines and good times.

All of my best days on the upper Allegheny have come when I caught the bait from the riffles in the river (blue sides/riffle runners).  Store bought bait and creek chubs/suckers from Pittsburgh creeks just don't seem to produce as well.  
 

While I have caught eye on store bought flatheads there is no substitute for chubs or runners. The later bait produces more and larger fish. In lieu of bait a jig and white 3 or 4" twister tail works.   

Imo, "full back" suckers are the best but it's hard to get them this time of year as they go dormant. We have used "riffle runners" also.

These riffle runner minnows are you guys seining them or actually fishing maggots for them ?
I only fish the Allegheny a few times a year near Kennerdale so that's new to me. 
 
I know over the years those dark black head fatheads are a waste of time for bait ......I'll take those silvery fatheads and toss those carp looking black heads out. 
 
I seine my own creek minnows locally and they are much better than bait shop fatheads, but I've never seen Riffle Runners that I know of.    

I fished tionesta Saturday.  2 other guys were fishing.  Sadly I didn't move a fish, but I was mostly throwing musky baits.   I fished the spill, the cribbage dam and the island boat launch.  I see they opened the walk-around behind the spillway outlet (good to know so you don't have to take the long walk through the campground).  Clarity in tionesta Creek to the river was about 4-5ft. River was about 3 ft of clarity.  Maybe someone else will have better luck and share their success secrets (PM me!)  Good luck out there...it was quiet and beautiful but the rocks were slick.  Great place...