Absolutely include it. The prologue is the beginning of your story. It’s the first thing your readers will set eyes on when they open the book, so it should be the first thing your agent sets eyes on when s/he opens the manuscript. You decided to launch the story with a prologue for a reason–it sets up a mood, maybe, or provides a vital plot tease before readers plunge into the main story. If you can omit it easily, I question its use in your manuscript at all. A prologue is your introductory handshake with your readers; extend that same hand to your potential agent.