Drexel University validates the amount:
Presidential Salary: $100,000/year + $50,000 expense account (refused
by Kennedy)
As DavePhD pointed out, that $50,000 could only be spent on presidential business, so the full amount that JFK could donate from his presidential salary was 100,000 minus taxes.
The History Channel backs up the claim that he donated his full presidential income:
6. He donated his congressional and presidential salaries to charity.
Kennedy’s father built a family fortune, and when the young politician
entered Congress in 1947, he earned sufficiently ample annual income
from trusts established by his father that he decided to donate his
entire legislative salary to various charities. Kennedy quietly
maintained the practice as president after becoming the richest man to
ever take the oath of office.
As The History Channel isn't focused on facts anymore, here's a list of supporting book quotes from this page:
"A millionaire by age twenty-one, Kennedy was our wealthiest
President. The only President besides George Washington to decline his
salary, he donated his to the Boy Scouts and Girl Scouts, the United
Negro College Fund and Jewish organizations." From: Page 67 "Lives of
the Presidents: Fame, Shame (and What the Neighbors Thought)" by
Kathleen Krull, read using the "search inside" feature at Amazon.com:
http://www.amazon.com/exec/obidos/tg/detail/-/015200808X/
"His $100,000 salary as President was being divided, after taxes,
among two dozen charities, including the Boy Scouts and Girl Scouts of
America, the United Negro College Fund, and the Federation of Jewish
Philanthropies. The schedule of contributions was worked out each year
during a short money meeting Kennedy had with a family accountant
named Thomas Walsh." From: Page 428 "PRESIDENT KENNEDY: PROFILE OF
POWER" by Richard Reeves, read using the "search inside" feature at
Amazon.com: http://www.amazon.com/exec/obidos/tg/detail/-/0671892894/
"He donated his entire presidential salary of $100,000 to charity,
ranging from hospitals to the Boy and Girl Scouts, to Jewish
philanthropies and retarded children's associations. In 1962, however,
he chose to make what were clearly strategically political
contributions with his private funds?the United Negro College Fund and
the Cuban Families Committee." From: Page 95 "The Kennedy White House
: Family Life and Pictures, 1961-1963" by Carl Sferrazza Anthony, read
using the "search inside" feature at Amazon.com:
http://www.amazon.com/exec/obidos/tg/detail/-/0743214730/
As for being a lot of money for that time: 100,000 USD in 1962 would have the same purchasing power as 783,894 USD in 2014. Yet nominally, it would still be worth only 100,000 USD.