Since this issue is often considered a human rights issue, a lot of human rights organizations have issued reports about police harassment and sometimes specifically about police harassment of transgender people. These often list their sources and are a good place to look for other resources.
Amnesty International has a couple of relevant reports:
There may be even more reports on the Amnesty International website (http://www.amnesty.org/en) in the library section.
The Human Rights Network () has another report on NYC Police Abuses from the New York City Coalition for Community Safety:
Susan's Place (http://www.susans.org/index.html) is a website for transgender people that has a wiki with reports and citations for incidents:
There was an article published in the New York Times in 2008 about a man who sued the NYPD after he was stopped and frisked: http://www.nytimes.com/2008/05/08/nyregion/08frisk.html?_r=1&scp=1&sq=Post%20Reporter%20Files%20Lawsuit%20Over%20Frisking%20by%20Police&st=cse
The RAND Corporation published a report on the NYPD's stop and frisk strategy. This is a link to a summary of that report, and it offers some useful statistics: http://www.rand.org/pubs/testimonies/2009/RAND_CT329.pdf