First, a myth: Travel agencies have access to cheaper flights
All flight tickets today are booked through so-called GDS systems, with the largest being Amadeus and Galileo. For example, when you search on Momondo, you'll see flights from companies that all book their flights through these very systems. This means everyone has the same prices on flights, and the only variation is the profit margin of the companies. For this reason, it's always cheapest to book your flight yourself, and it's a good idea to find your flight via a site like Momondo, where most ticket providers advertise.
The exceptions
Of course, there are exceptions to this. For example, if a travel agency has pre-booked seats on a flight (called allotments), their prices on those tickets are likely to be cheaper than the seats you can find online. These tickets can become even cheaper if the agency doesn’t sell them and offers them as last-minute deals. Allotments are usually not available on sites like Momondo.
Additionally, charter companies often charter entire planes at once. They control the ticket prices themselves, and therefore, they can sometimes be cheaper than scheduled flights. Charter tickets are usually not available on Momondo.