My guess is the hive with all the bees under the feeder simply has more bees in it. Hives with more bees will often hang around at the top of the hive for some reason. Maybe it’s warmer? Maybe the bees aren’t needed for cluster yet? Maybe there’s not room for the bees below? The main cluster of bees (with the queen) will likely be where the last of the brood is/was. I still have capped brood in my hives; no open brood.
1.) If the cluster is in the bottom box, they will have more food available to them to eat as they move UP in the winter. So conventional wisdom would say the main group of bees should be in the bottom box.
2.) They’re full or it’s too cold. I would pull the feeders like you have done. Actually I would have pulled them back in Oct, but now is better than later.
3.) In NY, you may want to wrap your hives or insulate. Otherwise there really isn’t much you can do at this point. It sounds like you’ve got the hives packed with food. Relax and wait until spring, go on a cruise, build new boxes for next year?