I live on the Upper West Side now. A friend stayed at The Beacon a few years ago and found the rooms tiny. I did a mattress run at the 4 Points Midtown when it opened and had a great rate; nice, but it's alongside the Port Authority Bus Terminal and can feel creepy later at night when the street is very quiet and you have to walk mid-block.
As for hotel's in my neck of the woods, a residential area right by the Museum of Natural History and the Planetarium, and across Central Park from the Metropolitan Museum of Art, here are a few. I've heard some good things about the Park 79, and their rates can be very good. Same for On the Ave.
Lucerne Hotel The
www.thelucernehotel.com - (212) 875-1000
Imperial Court Hotel
imperialcourthotel.com - (212) 787-6600
Hotel Belleclaire
www.hotelbelleclaire.com - (212) 362-7701
Park 79 Hotel
www.park79.com - (212) 787-3300
On the Avenue New York
www.ontheave-nyc.com - (212) 362-1100
Milburn Hotel
www.milburnhotel.com - (212) 362-1006
Hotel Beacon
www.beaconhotel.com - (212) 787-1100