A very comfortable bus line that works in that area is ETN (Enlaces Terrestes Nacionales). There is no direct bus in this company between Morelia and Puerto Vallarta, but you can take Morelia - Guadalajara (3:30 hrs - 290 MXP) and Guadalajara - Puerto Vallarta (5:00 hrs - 405MXP).
(The webpage is in the sources section)
Primera Plus is other option, they have a direct bus between Morelia and Puerto Vallarta, the buses are comfortable (not as the ETN ones) and it is cheaper (590 MXP)
(The webpage is in the sources section)
Other bus company called Autobuses de Occidente is almost certain to have a direct bus between those locations, unfortunately Autobuses de Occidente (not ADO, which is widely known, ADO is Autobuses de Oriente) has no webpage i know of. Autobuses de Occidente has some buses that are also comfortable (those are known as Via or Via Plus, being the later the more comfortable, as the Primera Plus ones) although not as comfortabale as the ETN ones, but they are cheaper, have more departures and more destinations.
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