Donna and Lisa have expressed one point of view, and for many people, that is the best choice. Personally, I like to devote many hours researching where I want to go and what ship to go on -- it's a huge pleasure to me. After deciding where, when and how, last time I checked Expedia, Travelocity, Orbitz, the cruise line site, two other online cruise agencies and the AAA agency locally. Expedia and Travelocity had the lowest prices including all taxes/fees (barely), so I booked through them and had a wonderful cruise -- exactly what I wanted. I also booked my flight and a hotel room for the night before the cruise. (After being the last one on board another cruise due to airline delays -- on a flight arranged by the cruise line -- I swore I would always allow plenty of time in the future).
For someone who isn't sure of what they want or don't have the time/inclination to do research, then a travel agency is definitely the way to go. In any event, check around for pricing.