Cornell Fisheries did quite a bit of research on Cayuga Lake's fisheries and sport fishing back in the 1940 and 50s. When I get time, I enjoy reading through the findings. It'd be nice to see some recent research done on the Finger Lakes, but most research these days is directed towards the Great Lakes.
Take these statements for what they are - finding that are over 60 years old and pre-date the recent invasives like zebra and quagga mussels, water fleas and gobies. There were also ciscoes in Cayuga Lake in the 1950s. My comments are in red.
1.) Studies found lake trout down as deep as 265' in Cayuga Lake.
2.) Smaller lake trout (under 20") are fairly well distributed in Cayuga Lake. Larger fish are migratory. (I think this is true on Seneca, Canandaigua and Owasco Lakes as well. Smaller fish tend to be homebodies.)
3.) Studies have not found a correlation between baitfish movements and lake trout movements. This goes against what most anglers/guides tend to believe, since we do typically find lakers around bait, but Cornell found greater numbers of baitfish in areas away from the heaviest concentrations of lake trout. Research suggests that spawning patterns play the largest role in the migration.
4.) Alewives are strongly favored by lake trout over ciscoes or smelt. This may have implications for the goby population. It may be that smaller non-migratory lakers will feed heaviest on gobies, but the larger lakers will likely keep following the larger protein source.
5.) Netting during the winter period resulted in no alewives taken in less than 40 FOW (feet of water.)
6.) Lake trout spend very little time around Taughannock Point. The show up in mid-September, spawning takes place into mid-November and then the fish migrate out of the area. Within a month there are very few lake trout inhabiting the point area. Can't say I'm surprised here. I rarely see many lakers taken after October on Taughannock Point, though at times the action can be hot in April/May. Probably due to the presence of smelt and alewives. The less smelt, the poorer the laker bite in the spring.
In the pre-invasive era, some smallmouth bass showed up in gillnets set for lake trout. Their depth ranged from 55' to 80' FOW with an average of 65'. Maybe some bass are deeper now. Though if there were many, we'd certainly catch a few while laker jigging.
Perch that wound up in gillnets were taken up to 70' deep. Average depth was 35'. Two small perch came off the bottom of the lake in 100' and 160'.
Rockbass were taken in gillnets up to 100' deep. Average fish taken were in 40' FOW. 3 were at 80'.