Pat McQuaid, speaking at the International Cycling Union (UCI) headquarters in Aigle, also took aim at reform group Change Cycling Now, which has called for him to quit, describing them as undemocratic and "agitators".
"It has been the best and the worst (year of my career), because London was the best, London was magnificent, and I got a lot of joy and pleasure out of London, and naturally the Armstrong affair was the worst," Irishman McQuaid, himself a former cyclist, told Reuters in an interview.
"It's been both. London is where I judge cycling to be, rather than Armstrong, because the Armstrong affair is back in the 90s."
Armstrong was stripped of his seven Tour de France titles, won between 1999 and 2005, and banned for life in October following a report by the United States Anti-Doping Agency (USADA).
USADA said that American Armstrong had been involved in the "most sophisticated, professionalized and successful doping program that sport has ever seen".
McQuaid, who has been UCI president since 2005, said he believed the public and media appreciated that the Armstrong period was outside his control.
"It deals with a period between 1999 and 2005 when most people now realize that the armoury in the fight against doping was much weaker than it is today," he said.
"Those guys were able to cheat and beat the system at that time because the system wasn't strong enough.
"Now we have the biological passport, where we do 10,000 tests a year at a cost of 7.5 million euros ($9.82 million).
"We invest in anti-doping and we have the no-needle policy I introduced, which means no teams or doctors are allowed to use needles except for medical necessity."
The UCI is also doing its best to get rid of the cheats for good, McQuaid added.
"We've also introduced a rule whereby any cyclist convicted of doping in a team can never come back into sport as part of the entourage," he said.
"That will take time to come through, but it means in 10 or 15 years time, that no entourage will have a member of a team who was involved in doping."
He pointed to recent reforms including the creation of a three-man independent commission, headed by former Court of Appeal judge Philip Otton, to investigate allegations that the UCI did not do its best to fight against doping during the Armstrong era.
The commission is to hold a hearing in London in April and produce a report by June.
"A lot of our critics said it wouldn't be independent and I think we've proven them wrong," said McQuaid.
"I think this commission is probably the most independent high-powered commission ever to study a sport's problem and I think they'll do a very good job on it.
"The commission will hopefully prove that we did do our job correctly."
McQuaid rejected a demand from Change Cycling Now (CCN), comprising former riders, journalists and anti-doping campaigners, which has said he should step down.
The group has been put together by Jaimie Fuller, an Australian who is chairman of the SKINS sportswear company, a cycling sponsor.
"I have to question their motives," said McQuaid. "The guy in charge from SKINS, he came into sponsoring cycling in 2008... For me, it's just a stunt to promote his company."
American Greg LeMond, who won the Tour in 1986, 89 and 90, said he was prepared to serve as an interim head of the UCI.
McQuaid dismissed the suggestion, saying: "That's not democracy. We are a democracy, we have democratic structures and everybody has to work to democratic structures.
"They are coming in with a completely different thing and when you look at the group which is sitting around, CCN, they're agitators who have always been individually agitating this, that and the other.
"I have a great deal of admiration for him (LeMond) as a cyclist. But since he stopped racing, he hasn't been involved in cycling at all, apart from a few businesses, so he's not really in a position to comment on what cycling is today." ($1 = 0.7641 euros)
(Editing by Julien Pretot)