Puerto Vallarta's main bus station is located north of the city just off MX-200 highway (Carretaria Pto.Vta - Tepic) at km-9.  If you arrive in Puerto Vallarta by air, you can get to the bus station (about 3 km away) by taxi or by taking a northbound "IXTAPA" city bus.  Most first class buses leave before noon, but there are hourly second class buses heading to the Costa Alegre.  If you arrive by airplane in the late afternoon, you will have to stay overnight before busing south, because a 1st. class bus trip takes 3-4 hours and 2nd class 4-5 hrs. You would arrive in the Costalegre in the late evening, a poor time to start looking for a hotel.

1) Flecha Amarilla  (322).221.0095,  (322).221.0867
2) Primera Plus  (322).221.0021  Toll Free Mexico: 01.800.375.7587
3) Transportes Del Pacifico S.A. DE C.V.  (322).221.1640 (also in old town at Insurgentes No.282,  (322).222.5622,  (322).222.1015)
4) Elite  (322).221.0848,  (322).222.6666 (Direct buses run form Tiauna to Acapulco. There are two First Class Express buses daily.  Stops in Melaque, but not Barra de Navidad)
5) Etn  PV to Guadalajara (322).221.0550  Etn  Guadalajara to Barra de Navidad.
6) Tres Estrellas De Oro
7) Grupo Estrella Blanca y Greyhound

Many budget travelers choose to travel from Puerto Vallarta to the Costa Alegre by regional (long haul) buses, as flights to P.V. are cheaper than to Manzanillo.  First class buses are recommended, as the cost is not much more than second class and have the following available features not always found on second class buses.  Toilets, air conditioning, movies and comfortable seats.  They are also, newer, cleaner and more punctual than other classes, as they are on a tighter schedule.  You may also reserve a seat location.  Regional buses have two employees on each bus, the driver and an attendant (swamper), who helps people on and off the bus, stores the luggage and serves drinks and snacks on long trips.