The battle for gay equality wages [unfortunate choice of verb - when I'm reading a lot of these letters on the trot, I'm reading quickly, and 'gay' + 'equality' + 'wages' first made me think you had a poorly constructed clause about a branch of trade unionism], yet most people are under the incorrect assumption that the battle for equality is all about gay marriage. It is so much more than marriage. It is about the right to exist and be accepted unconditionally as human beings with feelings, desires, and ambitions. It is a fight for the civil rights that have not been extended to the gay, lesbian, bisexual, and transgender communities. The past 10 years have been a tumultuous time for the LGBTQ community as steps have been taken both forward and backward. [This sounds a little like lecturing - you can presume that people in the publishing industry are fairly well read and are aware of social and political issues. Some of them even engage with these issues.]
My book, working title The Chronicles of Equality, examines the major arguments for and against gay equality and the advances made in the past decade. It is separated into three parts: Part 1 examines the major arguments of the equality fight including whether there is or is not a scientific basis for homosexuality, gay marriage and its effect on society, and the parallels gay rights draws to the fight for black civil rights; Part 2 provides a concise, yet detailed, year-by-year summary of the past decade; and Part 3 summarizes various outlooks and agendas of the major players in the fight for and against gay equality. There is a significant gap of non-fiction Gay and Lesbian literature that The Chronicles of Equality will address. Most of the literature examines gay rights history before the 21st century and is significantly outdated. [This sounds comprehensive but I don't know who you want your reader to be - as opposed to who your reader is likely to be. Your reader is likely to be someone who is already aware of the issues - those who are ignorant of the issues and wish to remain so aren't going to read it. So what's your intention in writing it - who is your ideal reader?]
In May 2011 I will hold a Master of Arts in National Security Studies and plan to study for my PhD in Conflict Analysis and Resolution immediately after. Throughout my undergraduate and graduate studies I have concentrated on subsets of national populations and their effects on domestic and foreign politics. This academic experience gives me the knowledge and research skills necessary to accomplish the goals of this book in a reader engaging rhetoric. [It also makes me think it's going to be an academic work, so you need to make it clear if you're writing for a trade/commercial audience or an academic one.] The catalyst for me writing this book was suffering workplace discrimination and harassment because of my sexual orientation, which brought me even closer to the already personal fight for equality.
Thank you for your time and consideration. If you wish to see the proposal for The Chronicles of Equality, please email me at AuthorAGL@domainname.com.
Overall: a fairly dense but competent letter. Try breaking up the first two paragraphs into smaller chunks - I'm being serious when I say we read a lot of these on the trot; it can get hard on the eyes when there's a large paragraph with lots of information.
What you haven't mentioned: word count and whether or not it's actually finished.