If you want to be close to the best cafes, you would probably want to be at or below 14th street (or in Chelsea, which may stretch above 14th a bit), though I don't know what hotels are around there (in fact, I don't know anything about NYC hotels at all!). There should be a good selection at/around Alphabet City and the East Village (Abraco, Ninth Street, Ost, etc.) but I'm just guessing here. For a better view of where things may be, try
http://www.espressomap.com. While that isn't an exhaustive list (see other NYC threads for that), it will give you a good idea of where to look. No matter where you stay in Manhattan, you won't be more than a 30 minute subway ride from great coffee (seems short for me). A number of places are also in Park Slope. Good luck!