The selection of San Juan Puerto Rico hotels is as big as you'd expect from any large city with choices for any type of travel, whether vacation or business.
Anyone who is planning on spending a good chunk of time on in Old San Juan is faced with any easy choice - either a hotel right in the middle of the old town (the best option) or close enough to get there easily.
The advantage of selecting a hotel in the middle of things is that you have access to all the bars and restaurants and don't need to do too much traveling each day to get to see what you want - hotels such as Hotel Milano, Gran Hotel El Convento, or the luxury Wyndham Old San Juan Hotel & Casino all allow you to stay in the confines of Old San Juan for your entire vacation if necessary.
If you're planning on a vacation that mixes Old San Juan with other locations then a hotel close to the old town but with easy access to the out of town highways may be a good option for you. The Caribe Hilton and Normandy Hotel both fulfill these requirements and offer upmarket accommodation with excellent communication with both Old San Juan and the airport.
Lastly, if your idea of a vacation is spending the day lazing by a pool one of the hotels in Isla Verde will be ideal. Destinations in their own right, you needn't set foot outside until it's time to go home.