Sounds great!
The bulk of guest houses / hotels are close to the coast and since you're looking into that type of business, that's where you should look.
Much depends on how much you have to invest, of course.
In the metro area (greater San Juan) the prices are higher. It's also the most popular area for tourists.
I personally would prefer the West coast (Rincon, Cabo Rojo) or on of the smaller islands off the main island (Culebra and Vieques)
When you come to the island and have enough time I'd say take a round trip along the coast - a couple of days will do, spend some time in the metro area and visit the small islands. That will give you a great first impression.
On the next trip explore the areas that you liked the best.