I have a Half top-a little pricey for what you get but no complaints. It Flips back like a sun roof in front but keeps the back end enclosed-think of a pick-up-with toneau cover backend- Jeep. You could run it year round.The back window also zips out.
With the rain most people just pull the carpet and drain plugs. Don't know where in NY you are-is theft an issue? do you have a garage?
There a re a lot of combinations of tops and if your Jeep is garaged may want to consider a frameless top that allows the back windows to zip in and out.
Here are a couple pics of tops I run -the snow is my half top-the other looks the same but is different is a bikini top with jammer and duster.