If you're flights aren't married segments, you don't have a choice - you must pick up your luggage in NY. I would also be afraid to make such a short connection as they aren responsible for you.
If the flight is a married segment, its nearly impossible to get them to check the luggage half way. I wouldn't be too worried- it can be convienent to lose luggage (amex insurance + home delivery). I also wouldn't be afraid of a short connection - the airlines are ulitmately responsible to get you to your destination - you might even get a better routing out of NY instead.
If you have a choice of buying them married or separte, its clearly safer to buy them together.