My biggest problem when renting a car in Manhattan is return policy - I usually only need it for a day or need to return it very late at night. Unfortunately, a lot of rental places around me only accept returns until 10pm or they charge an overnight fee regardless of return time. I was pleased to find that the Alamo on East 31st Street was easy to rent from and has a 24 hour garage return. This worked for my holiday decoration pick-up day - picked the car up in the morning and dropped it off after midnight when I finally finished my errands.
Price was okay - about $50 per day after all the taxes, etc. - and they gave me a non-gas-guzzling car. ;)