Channel Catfish are found in pockets throughout the region. To the best of my knowledge, none of the Fingerlakes have large populations of them. They occasionally turn up in Cayuga Lake, Seneca Lake and Otisco Lake. Like Black Crappies, there are a lot of catfish aficionados and there's no doubt in my mind that some of these people have illegally introduced them into various Finger Lakes. I recall a couple big ones being caught in Honeoye Lake some years ago. Canandaigua Lake, according to DEC documents also has a population of them. The bottom line is don't be surprised if you catch one, no matter where you are fishing.
The Cayuga/Seneca Canal system (mainly the Seneca River,) including Cross Lake, is loaded with Channel Cats. There are some large fish available! Oneida Lake has turned up cats in the mid-20lbs range and Cayuga Lake and the canal system are all connected waterways. Lake Ontario has a good localized catfishery, though they are concentrated around major trib outflows, like the Oswego or Genesee River and around the connecting bays/ponds. The bays towards the St. Lawrence River and the river itself also have some huge cats.
The population of cats appears to be going up in Otisco Lake. They've been present for at least 10 to 15 years. I'm sure they can reproduce there due to the currents in the narrows, murky water and cover (like logs.) There are plenty of baitfish in Otisco Lake, plus the oxygen depletion in the lake's depths may give the cats a bit of a predatory advantage.
As an aside, I grew up fishing around Irondequoit Creek and Irondequoit Bay from the 1970s through the mid 1990s. Back in the 1980s and prior, the bay water was considered devoid of oxygen below a certain depth, which I can't quite remember. But it was around 40' or 50' at most. Funny thing is I knew a guy who specialized in catching channel cats and he'd reportedly catch them on the bottom of the bay along the Rt. 104 bridge. They were on bottom in "dead water" that was over 60' deep!
Channel Catfish are far more adaptable than people give them credit for. Most people consider them to be a "bottom feeder," but at times cats behave like trout and salmon, suspending over deep water feeding on alewives. I know trollers who have encountered catfish (more than one!) while trolling in Cayuga Lake for lake trout. I've seen some cats in a pond feeding on the surface like trout!
What I do know regarding Cayuga Lake channel cats is that a few areas tend to produce them with some regularity. And I'm sure that if you put your quality time in and experiment, you'll probably find a few good "cat holes" on Cayuga. A few areas that produce catfish include the north end by Mud Locks and along the RR Tracks. Anywhere along the northern 5 or 6 miles of Cayuga Lake has catfish potential. When Cayuga AES is discharging warm water, catfish are around. I fished there at night with bait once and my buddy Dave caught a 23" channel. The south end of Cayuga Lake along the mudflats produces a few fish in the spring. A few also come from in front of creek mouths in May/June/July and lower Fall Creek tends to get a few after a heavy rain.
They are a sleek looking, hard fighting, very cool fish. Tops on the table too! I love catfishing though I don't get the chance to do it much. But if you've never caught channel catfish, give them a try. The shot on the species page is a big catfish that Perry caught on Otisco Lake. It was around 28" or 29" I think. Someday I'm heading to Otisco to go catfishin....