It is ALWAYS recommended that you REMAIN in the United States during the Naturalization Process. That way, NO questions can be raised about your application.
However, you have been granted the right to permanently reside in the United States, even as a foreign national pending Naturalization as a United States Citizen. This process does require that prior to filing your Naturalization Petition for United States Citizenship, you must reside in the United States for at least three continuous years...in other words, you can't be a 'commuter alien' and just visit the country on and off for three years and become naturalized.
So, it sounds like you have your three years put in by now..
If you have to leave the United States, I always recommend you check with USCIS before anybody on a pending Naturalization Petition leaves. The Service may want you to apply for a "Re-entry Permit", to explain your absence if you are going to be gone for an extended period of time or travel to some countries. I would not leave until your Naturalization application is received and there are no apparent reasons why USCIS would want you to remain.
Frankly, if you are just planning a short absence, you shouldn't have a problem, but check with USCIS first!
Here's the link:
I hope this helps.