It's not like Poughkeepsie is like Spanish Harlem. Not ALL of Poughkeepsie is bad. It's the home of Vassar College, (a Seven Sisters college) and Marist College.
OP, I know Poughkeepsie VERY well. Stay along Rt 9. I believe there are a couple Marriotts along Rt 9 (or along 44/55 - not as good of an area.) There are plenty of places along Rt 9 to eat, a couple of malls to go shopping & some movie theatres if you just need to pass the time for an evening. As a PP mentioned, there is the Culinary Institute, although I think you have to have reservations.
Which direction are you coming from? If you are coming from the Thruway from up north, Kingston is actually closer to the Thruway exit.
To get to Poughkeepsie from either direction from the Thruway, it would take you about 15-20 minutes. You'd have to get off the Thruway at either New Paltz: go across the Mid-Hudson Bridge to Rt 9, or via the Newburgh exit, go through Fishkill & Wappingers to get to Poughkeepsie.