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Law clerk at small firm. Wanted to give my two week notice today. I only work mornings and the attorney I work with/the boss isn't here. I'm not sure if he'll be here today or when this week. Is it inappropriate to do this via email?

I think that's fine. Just say you weren't sure when you would be in the office the same time as him and offer to talk to him via phone/in person if he needs to discuss the transition. I've had jobs where I gave my two weeks notice in person, and then had my boss follow up with me later stating that HR wanted me to send him an e-mail so there would be a paper trail. Ultimately, giving them sufficient notice so the work gets covered is more important than how you gave notice, especially if he's not always in the office.

I have done this, granted it was not at a legal job. Don't think it's a big deal but I would just offer to discuss this if they want the next time you come in, especially if you need the two week countdown to start today