The first thing to do is either contact a qualified travel company to make all your arrangements for you, or make sure you've personally booked everything ahead of time. Although many places in South America can be visited on a whim, the Galapagos Islands and Machu Picchu are very population vacation destinations, and you must book ahead. This is especially true if you're traveling during peak or holiday seasons, or if you plan to take a Galapagos cruise.
After you've ensured you have available dates for all your South America tours, hotels, and flights, the following is the best itinerary to follow. First, fly into Ecuador. You will have to arrive in either Quito or Guayaquil, because these are the only two cities that operate flights to the Galapagos Islands. Due to flight schedules and cruise departures, you'll probably want to spend your first night on the mainland, recuperating from your flight and becoming familiar with the Latin American culture. In the morning, you'll take a domestic flight to the Galapagos Islands, where if you've booked a Galapagos cruise, you'll be met at the airport and taken to your cruise ship right away.
Visiting the Galapagos Islands can be done either by a cruise or by an island hopping tour. There are many options for both types of travel in terms of what islands you visit, the time you spend, and what types of activities you wish to participate in. For this vacation plan, a 5 day and 4 night cruise is recommended. This length of time gives you ample opportunity to experience the numerous Galapagos ecosystems.
After the conclusion of your tour, you'll take a flight back to the Ecuador mainland, and then catch a flight to Lima, Peru. Lima is the only city in Peru that has an international airport. You'll spend a night in Lima, and perhaps enjoy a tour of this capital city. The next day you'll catch a flight to Cuzco, the capital of the former Inca Empire. Because of this flight connection, staying at a hotel close to the Lima airport is recommended.
When you arrive in Cuzco, you should spend the first time taking it easy, because going from sea level to the high altitude of Cuzco at 11,500 feet can be a struggle. The next day you can take your full Cuzco city tour, which includes visits to several ruins on the outskirts of the city as well as impressive colonial churches. The following day it is recommended you take a day tour of the Sacred Valley, which is the fertile region surrounding Cuzco, and also full of ancient Incan ruins. In the evening you'll take a train ride to the town of Machu Picchu Pueblo, the town closest to Machu Picchu. Staying here allows you to get an early start on visiting Machu Picchu the following day.
On your second to last vacation day, you'll wake up early and take a bus up to the entrance of the Machu Picchu citadel. Spend the morning on a guided tour to learn about the history of the site, and spend the afternoon relaxing and wandering around the ruins on your own. In the evening you'll need to catch a train back to Cuzco, where you'll spend the night. In the morning, you'll catch a connecting flight back to Lima, where you'll most likely stay in the airport until your final international departure back to North America.