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I clerked immediately after law school and I've now spent one year at a large DC firm. I'm thinking about lateraling. I know that everyone says it's best to lateral in Year 3 rather than earlier. Does that apply to clerks too? In other words, for the purposes of lateraling, do I count as a second-year or a third year (in January)?

If you a) want or need to lateral and b) have good options, there's no reason to wait until year three. Your marketability right now is a mix of your pedigree and substantive experience. Waiting for Jan won't matter in and of itself unless you can tick off some boxes during that time (take a depo, argue in court, etc)