I guess you could argue it either way. It comes down to the fact that we don't know exactly how teleportation works.* I could come up with a dozen in-game explanations that would prevent teleporting into an AMF, and an equal number that would allow it.
For instance:
Maybe Teleport works by opening a very short-lived planar gate between the Material plane and the Astral, and a second gate between that same Astral point and a distant Material location. Passing through the gates happens so quickly that it takes zero time, but the portal must be able to open at each location. Just as you couldn't cast the Gate spell in an antimagic area, the destination portal couldn't open in an antimagic area, and therefore the Teleport would fail.
That's just one possible explanation, mind you. Since the rules don't specify the mechanism of the "instantanous transport", the DM of a given campaign is free to decide on any specific mechanism he wants.
(*Does the Manual of the Planes clarify this question perhaps? I haven't read it all the way through yet.)