This is also household income, not personal income. Last I checked, the 1% mark for a single guy was roughly $192K/year, and for a household it was about $388K. If his spouse makes an equal amount, he could very well be in the 1%.
That's wealth. 1% income is $388K. Average wage income of people at the 99th percentile is relevant here, also. To assume that 100% of this person's income is coming from wages is probably a wrong assumption, esp. in this market.
Plus he mentions in the article (technically, in a comment) that his quarter-million figure includes insurance, 401k, discounted ESPP, and stock (which has a 1-year vest). It's not at all unbelievable that his actual salary could be as "low" as $150k.
That is NET worth not annual income. $250k is a very high annual income, and very few people attain this working for someone else. Most people bringing in that amount or higher are running a company.
That salary is not quite top-1%, but it is at least top 3%.