I will take the liberty of answering for Thomas here.
Most importantly, write a lot of comments, over years. Karma is primarily an odometer. I get 2X the karma per comment, but Thomas writes 4X the comments.
Develop a beat on which you are known as a source of expert, reliable knowledge. There are other security people on HN, but Thomas is fairly reliably stapled to the top of any thread about security. That is not not justified.
Write well. Have a voice. You can pick out most of Thomas' comments, and virtually all of his value-adding comments, immediately by his writing style. He's one of the five best writers on the site, without question. (Honest opinion rather than playing praise-my-friend-and-cofounder. It's not a close call.) You could ask him "Thomas, I am going to name one item in your kitchen. Write about it for two minutes. Ready? Parsnip, go." and it would be one of the ~10 best written comments on HN that day.
There exists an observation I can make here about choosing which threads to participate in, which would have the effect of increasing one's karma but which is not necessarily something HN wants to encourage. I have 100% confidence that "Boosting my karma score" is not the reason why Thomas chooses threads to engage in, but be that as it may, I'll add it for completeness: the high-heat low-light threads about nerd politics result in getting lots of upvotes for fairly little effort, regardless of whether you conform with HN's community norms or whether you are the designated contrary voice. (Designated contrary voice is worth a lot of upvotes if you do it well.)
Not related, but worth mentioning in case it isn't obvious: he really, really doesn't care about his karma score. Profoundly does not care. It happens to reward him for being "message board nerd" (his favored phrasing for this psychograph) but Thomas would play message board nerd for free and, indeed, at substantial cost.