To be honest, I’m not sure WHY you need to use a Travel Agent / Vacation Planner for this… technically you will be paying a premium for that service from them (it will be reflected in the price of the room)
Personally, I’d be calling up one of the larger Hotels and dealing with them for a “Group Booking”… where they put aside a block of rooms and your Guests call up by a certain date (a deadline) and do the booking at a preferred rate.
We are cruisers… and when in San Juan our favourite hotel is the Caribe Hilton… it is truly glorious… definitely Honeymoon worthy (we ourselves will be on a cruise for our own Honeymoon in January… and are planning to spend 2 nights at the Caribe)
BUT San Juan has many hotels… some better than others. Some are to be found in NEW San Juan, and others in or convenient to, Old San Juan.
If your cruise begins in San Juan, it really doesn’t matter where you stay, because the ship will be using the “International” cruise terminal which lies between the two parts of the city (not the pier closest to Old San Juan / and the Sheraton / Senor Frogs… as that pier is for ships that call on San Juan just for the day)
I suggest that you check out a map to get a good feel for the City… I like GOOGLE MAPS
GOOGLE Maps – San Juan = http://goo.gl/maps/OQgjf
You can zoom in and see where things are… and even ask it to find landmarks, Hotels etc.
If you switch over to Satellite View, you can see the cruise ships. The International Pier is to the right by the Airport…
Take a look at TripAdvisor ( http://www.tripadvisor.com ) and their Hotel Listings for San Juan. Then you can see how the various properties are Rated / Reviewed by Travellers just like yourself.
TripAdvisor – San Juan (Hotels) = http://www.tripadvisor.com/Hotels-g147320-San_Juan_Puerto_Rico-Hotels.html
There is also a map on that TA Page, that can show you where the various hotels are located.
Hope this helps,