Guayaquil

When my wife and I fly in late, we always have a hotel room for the night and the hotel picks us up at the airport with their shuttle.  Sorry I don't remember the name of the hotel. My wife is asleep right now.  She knows the hotel we stay at.  It is in downtown Guayaquil.
I highly recommend that you rent a car for your trip.  We have done similar trips in the past.  You can travel to all of these locations using the buses which are similar to the Grayhound buses in the US but once you get to the cities, you will have to use taxi's or walk.  Having a rental car will give you more flexibility.  Rent the car from the US on the internet.  Pick it up at the airport the morning after you arrive.  You don't want to have to deal with renting a car at midnight and then trying to find downtown and find your hotel.  Take the shuttle to the hotel then take the MetroVia to the airport and deal with renting the car after you have rested and had a good breakfast.  you can call my wife Rosa and myself at our US number (919) 848-7839 and she can fill you in with all the details you need.  She is a Guayaquil native.
Hope you have a great trip.
Fred Johnson