Anyone know of any other sites like VRBO and AirBnB?
In NYC there's been a crackdown on those types of websites (especially AirBnb) because it's apparently illegal for one to offer their house up for very short-term accommodations (stealing business from hotels, etc.). I'm not sure how that's affected the listings on those sights but if you're not finding a whole lot, that may be why.
If you're not averse to hostels, there are a couple on The Bowery (The Bowery House and Bowery's Whitehouse Hotel, which was recently written up here: http://ny.curbed.com/archives/2014/03/26/spending_the_night_inside_nycs_worst_hostel_cost_45.php?skip_mobile_check=true) which are quite affordable.
As far as other websites, check out www.directloft.com. I used them once and have recommended them before.
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www.homeaway.com is powered by VRBO I believe. Couchsurfing.org is a good one for free accomodation, but requires you to do some work before others will take you in.
Depending on your budget, you can find some pretty cool places to stay using Hotels.com or the Hotel Tonight. There can be some pretty cheap rates for some really nice places. The only downside is that you might have to switch places frequently if you are staying long term. I used the service extensively for several weeks while traveling for work in the city and stayed at some pretty cool places.
You can find some great prices, accommodations and location at the Chelsea International Hostel in NYC.
Use Viator.com for booking tours and activities in New York!