There are many congregations that support transgender and gender variant people.  A good place to start looking is at LGBT welcoming congregations in your area, such as in the directory of the Institute for Welcoming Resources (a project of the National Gay and Lesbian Task Force):

http://www.welcomingresources.org/directory.htm

However, not all congregations that call themselves LGBT-friendly have actually done much work on transgender issues.  So be careful and take care of yourself.  It may help to call ahead--or to take a supportive friend with you when you first visit.

Many congregations are inexperienced but eager to learn about your journey. Trust your gut reaction about whether a congregation is able to treat you with respect and compassion -- even about aspects of your journey that they may not understand.

TransFaith is exploring the development of a directory of "Trans-Safe" congregations.  We welcome your input (e.g. does your congregation have experience with ministry in the transgender community?) and support (e.g. financial resources are essential to building a useful network).

Meanwhile, HRC has produced a short, useful brochure that highlights issues you may want to consider before you disclose/come out.

Living Openly in Your Place of Worship (PDF)
http://www.hrc.org/documents/livingopenly.pdf