Just write the email right now asking for the letter. If you feel sheepish about "asking over email," just say "I'm sorry I didn't have a chance to ask you in person, but because we're on break, I wasn't sure how long it would take to set up a meeting."
The number 1 courtesy issue with asking for letters of recommendation is promptness and giving your writers as much time as possible to write and submit the letters. I think that completely overrides any concerns about medium, especially when it's not necessarily easy to meet with the person in question right away. I'd certainly much rather get an email about submitting letters than to go to the trouble of specially setting up a meeting with some amount of delay. (In fact, when students do ask me in person, I usually tell them to sent me an email about it so I have a permanent record of the request).