Relocating to San Diego ... Any advice on where to rent a home?

Check out the Automated Housing Referral Network. Also, take a look at Trulia.com

https://www.ahrn.com/index.php

I reside up in Oceanside, CA. It is a little drive, but it is very close to Camp Pendleton and a great commissary and MRX where I do all my shopping. Here are some rental management companies that could help you out:

http://www.cpmteam.com/

http://www.barbaramclain.com/

http://carlsbadproperties.com/

Also look at lincoln military housing i think its the same houses as ahrn but its worth looking at but my personal preference is chula vista its a good area close to shopping centers and its not far from coranado