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Nope, I personally don't think it's 'okay' to put that you prefer skype interview.
The employer is the one that dictates the terms of the interview, not, I repeat, NOT the applicant.
Some employers may, if they see that an applicant lives far away in another state, conduct a skype interview (as happened to one guy we interviewed a few weeks ago, and to a friend of mines who interviewed at one of my old jobs while he was living on the east coast).
But things like Skype are meant only for situations of that sort, never to replace a face to face interview if at all possible.
Completely agree that it wouldn't be appropriate to put in your cover letter that you'd prefer a Skype interview. Honestly, if I read that, I'd wonder why- particularly if you did live in the area. As others have said, applicants don't get to set the interview terms. Good luck.