1.  Geert Mak’s insightful and concise Amsterdam:  A Brief Life of the City is your first stop. He is erudite but never needlessly obscure, and his style is engaging, giving a sweep of the history of the city.  You can almost get through the book on the plane if you are a fast reader.  Here’s a quick interview with him talking about the city and how it shaped him.
2. A newer book with a somewhat different take is Russell Shorto’s Amsterdam:  A History of the World’s Most Liberal City.  He’s an American living in Amsterdam who surveys the city’s origins in terms of its major contributions to the idea of individualism and human rights.  Because he ties all this to the development of the US, it may be of particular interest to American readers.  His style is accessible and fun to read.
3. Go back to Anne Frank’s Diary of a Young Girl.  Her situation was in many ways atypical of people in hiding, since she was a precocious and remarkable writer with a father whose wealth and foresight provided many comforts, and whose friends were ready to risk their lives day after day.  What was all too typical, however, was Anne’s basic predicament:  being deprived of her liberty in almost every way, only because she was Jewish.
4. The best overall account of the Nazi Occupation and its impact in English is Bob Moore’s Victims and Survivors:  The Nazi Persecution of the Jews in the Netherlands:  1940-45.  While the book has a scholarly bent, it is clearly written and covers the grim story thoroughly but not exhaustively.  It addresses the questions of how these years were seen and written about by historians just after the war.
5. The classic, eminently readable work is Jacob Presser’s Ashes in the Wind:  The Destruction of Dutch Jewry, a devastating, telegram by telegram account of how the Nazis and their Dutch collaborators succeeded in spite of the resistance – and how the Jewish people who survived did so.  Because Presser experienced these events personally and occasionally breaks into his own voice, this account is much more than an objective historian’s work, although it’s that, too.  Presser was commissioned to write this study by the Netherlands World War II Institute (now the NIOD Institute for War, Holocaust and Genocide).  It took him twelve years rather than the two which he first intended.
6. Remembering Jewish Amsterdam by Philo Bregstein and Salvador Bloemgarten is a lively book based on interviews and oral histories with Holocaust survivors, significant because it evokes the world of a diverse community of Jewish people originally from many places, representing the full range of economic and social class.  They were at the pinnacle of medicine, music, and the arts, but also they were peddlers in the streets.  As we mourn the murder of these lively characters, we are aware that they are not just ghosts, but were real, living people like ourselves who contributed to making a great city what it was.

While it’s not set in Amsterdam, here’s a classic you may well have read, but it bears another look:  Corrie ten Boom’s memoir The Hiding Place, which shows the courage of a deeply Christian watchmaker’s family in nearby Haarlem.  While some people of faith, and most of the institutional churches in the Netherlands, did little to take action against the Nazis, the ten Booms are a sterling example of those who did.  It is also fascinating to take the short train trip to Haarlem and visit the ten Boom’s actual home.  You’ll see how tiny the hiding place was — a much more typical size than the Franks.

There are many, many other worthy books.  This is only a start.