"We're really, really pleased," Thomson told Journalism.co.uk, describing the creation of the paywalled site, which was launched just over a year ago, as a "step into the unknown".
He added: "We believe it's the right way and that our content is worth paying for. We are unapologetic and our strong figures show readers feel the same."
The Guardian and BBC took a joint award for best site for news-led journalism in the Press Association-sponsored awards, which recognise the best online journalism.
Emma Barnett, digital media editor of the Daily Telegraph, took home the award for digital writer of the year.
BBC London did well, taking a joint award alongside Mashable for the best use of social media and for best crowdsourcing or citizen journalism, for its writing on the London tube strikes.
The best podcast was also a BBC win, going to the Non League Football Show, which gives sports fans a platform to converse with each other.
The award for best brand development went to Mail Online for the successful US edition.
The chairman's award went jointly to the Nursing Times site and Press Gazette. Chairman Noel Young selected the Nursing Times for demonstrating an unprecedented success over the past year, in terms of traffic, engagement and revenue, despite being a small niche site. Young described Press Gazette as "an excellent, tight, news-led site".
Smaller sites were also recognised: Physics World won best specialist site for journalism; @naturenews took home the award for best twitter feed and FoodBev.com won in the best commercial innovation category for successfully charging for their digital editions.
International sites were also recognised, with the Huffington Post, which is due to launch a UK edition on 6 July, taking home the award for best commentary or blogging.
A full list of winners is at this link.