The only time that you're likely to get better pricing through an agency is if that agency has access to bulk tickets, and passes that savings on to you.

I use a travel agent from time to time, and pay a small extra fee when I do. There are multiple reasons for doing so, including the expertise of the agent, lack of time on my part, complicated itineraries, and having a resource to fall back on if things go wrong. A good travel agent can be worth their weight in gold.