Diversity just means reality: a story that actually relates to the world we live in. The white, able-bodied, neurotypical, twenty-something, cis, hetero, male stereotype got old a long time ago. If you’re totally confused, go look up Malinda Lo and Corinne Duyvis for a good introduction.
If your novel features diversity in the forefront (a Down’s Syndrome protagonist, a queer princess, an older grandpa who kicks butt), you need to put that in your query. Mention it when you tell the agent what genre your book is.
But more than that, you can put it in the email’s subject. Most agencies require your subject be some form of “Query for [Agent]: [Title of Your Book].” There’s absolutely nothing wrong with starting out “Diverse Query for…” When I see queries like this, I read them first because diversity is so needed in the industry. Plus, chances are if you’re writing diversity you’re also writing something original.