Yes, it's safe. I went through the body scanners when I just conceived (less than 4 weeks) and another time when I was 9 weeks pregnant. My baby came out fine. It's a lot more convenient to walk through the scanners than to request for a full body search, though it's your choice, really. http://www.babycenter.com/404_is-it-safe-to-walk-through-airport-screening-machines-while_2616.bc
For me, I will avoid it although the custom officers and internet mentioned the radiation is minimal and not harmful. What I do is, I will inform the officer that I am pregnant and I do not want to go through the scanner. They will let me walk through another path and let female officer do a full body search and check on me. So far, I have no problems doing this at airports.
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thanks