Clean, safe, well-located pilgrim's lodgings
If you need a clean, secure place to lay your head for under $100 in downtown Manhattan, this is it. For that price, you get a humble lodging - a room with a singe bed, a desk, a tv and a sink, with a shared toilet and shower in the hall, brilliantly located right off Union Square. That was all I needed (except the tv) - and with a little imagination and all of Manhattan waiting outside, who needs more, really? They have wifi and computers for use on the mezzanine, free coffee in the lobby, laundry and vending machines in the basement. Note that visitors are not allowed above the lobby level. No extra charges, taxes or hidden fees, although donations are welcome.
This outfit is run as a nonprofit hospitality ministry by Lutherans, but they welcome anyone and are very pleasant and not at all pushy about the religious mission. Services are held in the ground-floor chapel at 11am, if you are so inclined. The front desk staff are pleasant but not obsequious, and they are flexible about holding luggage before check-in (3pm) or check-out (11 am) times. 
No food is served on the premises, but Joe Junior's was the staff recommendation for breakfast -- a most excellent and inexpensive short-order dive.