We booked out vacation through SellOffVacations.com. We tried 3 travel agencies and a number of web-based reservations systems, but found SellOffVacations.com to be the easiest to search, and had the best prices for what we were looking for. They were professional an efficient when we booked.
Our actual vacation package was from Vacances TMR. Everything went smoothly, and the TMR representative in Puerto Vallarta was there when we needed them, and left us alone the rest of the time.
There are lots of web sites with information on Puerta Vallarta and the Jalisco region, since it is such a popular desination. Here are a few we found useful:
- PuertoVallarta.net
- AllAboutPuertoVallarta.com
- VisitPuertoVallarta.com
- VallartaOnline.com (I found this site the particularly useful)
We stayed at the Hotel Tropicana, right on Los Muertos beach, in the romantic zone, also known as "Old Vallarta". At the back
of the hotel, we could laze on the beach under a palapas (a large
umbrella of palm fronds). From the front we had acess to the
village with its markets and hundreds of restaurants.
The Hotel Zones, and Marina Vallarta are at the north end of the town. The larger chain hotels, and all inclusive packages tend to be in these areas. While the hotels are grander more modern and resorts luxurious, you are also in a "strip" away from the town, and won't be able to walk anywhere.
If you stay in the Romantic Zone, (and I'd highly recommend it!) then I'd advise against an "all inclusive" deal. There are hundreds of restauraunts of all kinds within a few blocks, and you won't want to be stuck eating the hotel food.
Our day tour to the San Blas and the La Tovara nature reserve is run by Trafic Tours. Trafic Tours does not have their own web site. You can book through your tour company, hotel, agent selling tours. in the area

Pueto Vallarta viewed from Banderas Bay
The romantic zone, where we stayed, is to the right-hand side