We recently returned from our honeymoon which took place aboard a Carnival Cruise. We checked prices for the cruise using the usual online travel sites like Travelocity, Expedia, Orbitz, as well as cruise-specific sites. We also checked the same cruise via Carnival's website. Then we called an independent travel agent to see what they would offer us, price-wise, for the very same 4 day/4 night cruise that we were interested in. The travel agent was only a few dollars higher than the third-party travel sites or directly via Carnival.
We ended up booking our honeymoon cruise directly via a Carnival agent by phone, and had a great time at a pretty reasonable cost. Carnival didn't charge any more or less than the third-party travel sites, and was a little bit cheaper than going through an independent agent. However, you may wish to book a cruise or resort honeymoon via an agent especially if that agent specializes in either cruises or resorts (depending on your desires), and you have no idea which cruise lines you want to sail or which resorts you might want to honeymoon in. If you have a good idea where you want to go, how you want to get there, and you have a great deal of travel experience - then booking directly via the cruise or resort website (actually calling and reaching a live reservations agent is better) is the way to go. Our Carnival reservations agent was very helpful - but again, we already knew who we would be sailing with on our honeymoon. Happy honeymooning!