How to (smartly) leave a postdoc early?
If you have a good relationship with your advisor, consider informing him or her early in a very respectful way. He or she will appreciate you took the time. Why give them a reason to (potentially) write a less than stellar letter?

If you do NOT get a letter from your current advisor and go for another post doc, yes it will absolutely raise a flag. You could expect the topic to come up, or the interviewer make even contact your advisor directly.  However, if it really only has been a few months, simply stating the environment/locale/work/etc wasn't matched may be sufficient.