Chris, in NY, I've had luck with hotels around the Bowery/ Chinatown area. I've stayed at the Hanbee (Best Western), very nice, and sometimes less than $200. Stayed there 3 times, also great food in the area.
http://www.tripadvisor.com.au/...k_City_New_York.html
Also, if you decide to go via Harrisburg train station, the GG1 is worth seeing.