How do you decide how much rent to charge? How often do you raise the rent, and by how much? Is there a legal limit to the percentage it can be increased? I have been searching for the answer to this for NYC, but I haven't been able to find anything that does not apply to rent-stabilized units or units in large buildings. Thanks for any info.

Non rent control or stabilized ... you can charge what ever you want. Doesn't mean they'll pay.
Research similar apartments in the area.
Or just sell the frickin thing