This is very interesting and there are small fish species that will persist in Lake like habitats. Some of the suggestions you have gotten were very good ones, logperch are a great idea. Also johnny darters will persist in lakes as well. Iowa darters are also a great suggestion and it might be worth looking into if they could be legally acquired and stocked or what steps maybe would need to be taken to do so. As far as Cyprinids that might work... you say there is a lot of vegetation and clear water so my mind goes straight to blacknose and blackchin shiners but these likely would also require the same checking out the legal steps like the Iowa darters. (I might know a source for all three of those of captive raised stock 
) Both shiners are probably protected in PA just like Ohio. I have often wondered though if they could be established in clear quarries that had some vegetation.
Other minnows that should work if there is a lot of cover would be bluntnose minnow, and possibly spotfin shiners. Also golden shiners will use the vegetation and should persist if enough cover is available. I would not use fatheads even though they may work because although found in your area now they probably are not native in that area, they just have become really widespread due to bait releases. Last one I would check the distribution out on and see if they are in your area is northern redbelly dace. I don't know if these would work but I know their habitat use is quite different from other Chrosomus sp. I am not sure about their PA distribution and if they are in the watershed your talking about.
You could try to diversify the sunfish community by adding warmouth, rockbass, more pumpkinseeds, and smallmouth bass. Of all of these I would think the warmouth may have the best chance of establishing a small population. In presence of bluegill they persist in small numbers if a lot of vegetation is present but never become a dominant part of the community. Based off your initial list I can tell this is in the Allegheny River basin. There are old records of Longear too but they do not do well in the presence of largemouth and bluegill and are also protected in PA probably won't work and more red tape.
Paddlefish are also a common stocking in quarries and although they do not reproduce they do seem to grow and persist for long time periods. What Matt pointed out is a great idea and it is worth contacting them because they may know what the legal requirements would be for your area. They just did the same thing with a dive quarry near me.
A few musky or walleye might be interesting but I would not expect them to reproduce in a quarry so they would be a novelty much like the few northern pike already present. These both are available commercially but as already stated local stock would be most ideal if possible.
Yellow perch also are a good idea and likely to persist and reproduce.
Also longnose gar are present in the Allegheny and might make an intriguing addition. Might reproduce minimally but would also be more of a novelty and you would probably have to catch your own.
With anything you would have to catch yourself you need to make sure there are no legal issues with acquiring your own local stock if legally captured and transported to the site. This is a very interesting project and could be a lot of fun but you just need to be cautious and calculated about what you do. I have done a few stockings like this but they go much better when you have an empty water body to start. It is difficult establishing new species into an existing community. Some of these ideas may work well and some may completely fail but you won't know without trying.
. I might shoot an email to the commision to see if it'd be legal to stock some.
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