here are some relatively cheap suggestions downtown. check for online specials and discount codes.
hampton inn http://hamptoninn.hilton.com/en/hp/hotels/index.jhtml;jsessionid=HNUDHGDZLYSOGCSGBJBNEWQ?ctyhocn=NYCMHHX
fully furnished apartments for about the same price as a hotel are found here http://www.metro-home.com
I heard about a pool bar at hotel grace near times square – fun! http://nymag.com/listings/bar/The-Bar-at-Hotel-QT/
what was a hojos on houston street below turned into the gem hotel http://thegemhotel.com/soho/index.iml .
chelsea lodge http://www.chelsealodge.com
chelsea savoy hotel http://www.chelseasavoy.com
larchmont hotel http://www.larchmonthotel.com this is on 11th street between 5th and 6th avenues – the catch is that for the cheapest rooms, you have to share the bathroom
cosmopolitan hotel http://cosmohotel.com it is across the street from the WTC site, lots of europeans stay there.