Do you need a romantic kind of hotel or cheap/clean/cheerful?
If cheap/clean/cheerful is acceptable, I always recommend the SIHNYC. Seafarers' International House. It houses the Lutheran mission to the harbour. Last active seafarers' mission in NYC. There is a clientele of sailors there, receiving services of various types, usually a decent representation of German tourists and Lutherans from across the world (they advertise in Lutheran magazines).
It's affordable and has LOCATION !!!
It's just off Union Square near Broadway and 14th. The next block is Lee Strasberg Way - interesting little theatre stuff going on there. Often young actors draped around, waiting to audition.
Handy to subway - walking distance to theatre/shopping if you enjoy a city stroll. Some fabulous restaurants nearby and it's close to the Strand (awesome incredible bookstore). There is a Trader Joes and a Whole Foods within very short walking distance - so you can stock up on water/yogurt etc and keep them in a little room fridge.
I've stayed there 3 or 4 times in the last 5 / 6 years. A few other A2k'rs have stayed there (most recently JoefromChicago, I think). Walter Hinteler stayed there with us when we had a bit of an A2k get-together.
It looks like a regular hotel - with slightly more floor space in the double rooms than other hotels in the area that cost 3 - 5 x as much per night.