Is fish cleaning included?
Most crews will fillet and bag your catch at the dock. Whether it is included or tipped for varies by boat, and no captain can store fish for you afterwards.
Cleaning and bagging at the dock is normal practice here and is often treated as part of what the crew does rather than a line item. Some operators list it explicitly; where it is not listed, assume it is a courtesy and tip accordingly.
Once your fish is bagged it is yours to deal with, and it will not keep long in this heat. Many restaurants in Puerto Vallarta will cook your catch for you if you bring it in the same day — ask the crew which places near the marina do it.