On a recent appearance on The Late Show with Stephen Colbert, The Walking Dead Actress Danai Gurira (Michonne) was asked about what her pick for most zombie proof shelter would be. Her pick makes total sense.
Danai Gurira: It's an island right? You get there, you clear it out, and you chill. You figure out how to sustain yourself through agricultural means, and you know
Colbert: I'm going to write this down
Gurira: Write this down man!
I have to agree, although it can't be a large island. It has to be a tiny one, small enough where you could actually defend it properly without any stragglers getting in. At this point, that might be the only place to restart civilization.
Though really, if you think about it, you could really defend a variety of places from the undead. The only issue has been defending it from other living people. The prison was great until the governor attempted to invade. Alexandria was fine until the Wolves ransacked it. Heck, the farm was fin...yeah no, the farm was bad. Forget I mentioned that.