Taken from my AH profile page where you can find more recommendations for example on ships and navigation of the period:

Suggested Books and Articles

Portugal and Portuguese Empire

Books

• Portuguese Seaborne Empire 1415-1825 (1969) by C.R. Boxer. Boxer is till this day the accepted authority and this book is still the reference book for the Portuguese empire from it's beginnings of expansion to the breakaway of Brazil.
• Prince Henry the Navigator: A life (2000) by Peter E. Russel. The ultimate biography of Infante Henrique in English, who was one of the key people in kickstarting the Age of Discoveries which lead to his elevation to mythical status during the 19th century. This book tries to reveal the 'real' Henrique and goes less into the details of 'his' discoveries (conducted by his authorization by other people) and more into his own life, motivations and decisions.
• Foundations of the Portuguese Empire 1415-1580 (1977) by Diffie and Winius. Detailed book detailing the beginning and peak of the Portuguese Empire in the 15th and 16th century. Accent on the events, battles and general military and political developments. Good also for general review of ships, navigation methods, weapons and equipment.
• Portuguese in Asia: 1500-1700 (2012) by Subrahmanyam S. Accent is on the economy and politics of the Portuguese presence in Asia. It is full of data and statistics about trade, shipping, earnings, costs and the general way the Portuguese presence in Asia was set up. Also gives slightly more information about the Asian surroundings (but the focus is still on the Portuguese).
• The Portuguese in India by M. N. Pearson. Focuses in entirery on Portugal on Indian subcontinent and their organization and administration.
• A History of Portugal and the Portuguese Empire: From Beginnings to 1807 Volume I and Volume II (2009) by Disney A.R. A great overview as well as introductory reading to Portuguese history. You can easily jump to chapters one is interested about. Volume I is chronological history of the mostly mainland Portugal, while Volume II goes into greater details about their colonial holdings.
• Portuguese Sea Battles - Volume I - The First World Sea Power 1139-1521 by Saturnino Monteiro
• The Christian Century in Japan, 1549-1650 by C.R.Boxer on archive.org. Chronicles the work of Portugese and Jesuits in japan until seventeenth century and closing of Japan.
• The Cambridge History of China, Volume 8, Chapter 7: Relations with Maritime Europeans 1514-1662 - chapter dealing with early Sino-Portuguese contacts
• Merchants and Rulers in Gujarat: The Response to the Portuguese in the Sixteenth Century by Paerson. More insight into Gujarati society and their interactions with the Portuguese upon their arrival. Gujarati were the merchants of the Indian ocean, whose trade networks spanned continents. Full free Google book.
• Decay or defeat ? : an inquiry into the Portuguese decline in Asia 1580-1645 by Ernst van Veen -doctoral thesis about the causes of decline of Portugese empire. Mostly about shipping and economy, full of data and comaprison with VOC

Primary sources

all free and available online

• The Chronicle of the Discovery and Conquest of Guinea. Vol. I and Vol II by Zurara/Azurara. English translation (available free from Gutenberg) from text originating in ~1450s. Account of early Henrican voyages of discovery (until 1450) by Henrican offical chronicler Zurara (or Azurara).
• Original Journals of the Voyages of Cada Mosto by Cadamosto originally written ~1460. English translation in "General History and Collection of Voyages and Travels Volume II" by R.Kerr (1824). Alternative translation in G.R. Crone, ed. (1937) The Voyages of Cadamosto and other documents on Western Africa in the second half of the fifteenth century. First hand, reliable, account of several voyages to Senegal and Gambia in 1450s by Venetian merchant Alvise Cadamosto in service of Henry the Navigator.
• The journal of his first voyage to America by Columbus, Christopher - 19th century translation so possible mistakes corrected in modern versions. Also the original journal in its original form does not exist, these are the notes compiled by De Las Casas from the original.
• A Journal of the First Voyage of Vasco da Gama 1497-1499. English translation by Ravenstein E.G. Hakluyt Society (1898). original journal of Vasco Da Gama's journey to India and back with descriptions. Stops little before final arrival to Portugal.
• Voyage Of Pedro Alvares Cabral To Brazil And India by Greenlee, William (Hakluyt Society 1937). Detailing the events of the Second Portuguese expedition to India. Not the original journal of the voyage but has some collected letters.
• The Letters of Amerigo Vespucci and Other Documents Illustrative of His Career English translation by Markham, Hakluyt Society (1894). Note that the first letter is now mostly considered fabrication of the early 16th century, and there is some doubt if the first voyage even took place.
• The travels of Ludovico di Varthema in Egypt, Syria, Arabia Deserta and Arabia Felix, in Persia, India, and Ethiopia, A.D. 1503 to 1508 - travells of an Italian merchantmen through Arab and India lands in about the same time Portuguese arrived in India.
• The Suma oriental of Tomé Pires : an account of the East, from the Red Sea to Japan, written in Malacca and India in 1512-1515 written by Toma Pires around 1515. English translation by Hakluyt society (1944). A Portuguese travelers account of the lands and countries in Asia in early 16th century, some visited, some just recorded from others. Description of each country, their rulers and military strength, and commercial and trade analysis for each.
• A Description of the Coasts of East Africa and Malabar in the Beginning of the Sixteenth Century, by Duarte Barbosa by Hakluyt Society (1860s). Description of Indian Ocean around 1515-1520. Alternate edition (1918): Vol I and Vol II
• The First Voyage Round the World, by Magellan - published by Hakluyt Society (1874). Collection of translated documents relating to voyage of Magellan
• The Discoveries of the World from Their First Original Unto the Year of Our Lord 1555 by Galvão, António. Chronicles of entire history of all discoveries from dawn of time, including Portuguese ones.
• Letters from Portuguese captives in Canton, written in 1534 & 1536: with an introduction on Portuguese intercourse with China in the first half of the sixteenth century by Ferguson. Collection of letters from captive portuguese about China and the events surrounding the Portuguese embassy to the Emperor 1517-1522. These letters are the main source of what we know of early Sino-Portuguese contact.
• The Canarian; or, Book of the conquest and conversion of the Canarians in the year 1402 - chronicle of the conquest of Canary islands by the French Jean de Béthencourt and Gadifer de la Salle.
• Hakluyt society has translated many primary sources of discoveries, exploration and voyages in English. Many are from 19th century, early 20th and their copyright is expired and are now available for free on sites like gutenberg.org or archive.org. Full list with links