My biggest reason besides the cryosleep that indicates she is an android is the design. David has the yellow hair and wears shades of cool blue and cool gray that is also tied into the ship's design. Meredith likewise has the same color scheme. They are both hardware just like the ship. She walks like David. She is strong like David, and she doesn't display human compassion like when she burns up Charlie (Elizabeth tells David her compassion is the reason that she is human and he isn't). There will be those who say, what about the other scientists who had blonde hair? But those scientists were seen yacking after cryosleep or slumped over; and they weren't given the prominence Meredith was given. Meredith wasn't.
Furthermore, the subtext in the film is that David knows she is an android and she doesn't know it, just like Rachael in Blade Runner. David gets a kick out of her trying to establish her human superiority over his robotic inferiority (when she threatens to cut his cord) because he has intimate knowledge of her fabrication. The look on his face is that he wants to tell her but his orders prevent it. When we see David getting his orders from Weyland about "Try harder" -- it was evident by the skewn composition that we were seeing it from someone else's point-of-view. But the point of view was detached and withdrawn.
Also, it involved a level of stealth that clearly verged on predatory or suprahuman. Then the revelation was that Charlize Theron was the individual who had snuck up on him and was watching him. When is a human character in a Ridley Scott film ever able to sneak up on a non-human character in such a predatory way unless it was alien or android? In this scene, the power is clearly Charlize Theron's. Not just in her actions but in the way Scott codes her as a silent stealthy creature. It's clear that David and Meredith are related in ways the others are not related because their movement, their mannerisms, and their attitudes are synchronized. As actors, they are playing off each other, so Theron tries to humanize Meredith in a way that is far more advanced than David.
Lastly, we can see the expressions in Weyland's face that when she tries to use emotional pleas for him not to go and see the Giant, that her emotional pleas ring hollow. Firstly, it's the way she says father -- though it's an appeal to emotion, it is awkwardly uttered and awkwardly timed. She was directed to say the line as if it lacked proper emotion. As if it were the thing to say. Only a machine that lacked emotion but were trying to find a way to make an emotional appeal based on its programming would do so in such an apathetic manner. Weyland's physical reaction is that her appeals ring hollow because he knows she is a hollow woman at her core. Far more advanced and emotionally sophisticated but not sophisticated enough. Some argue that Weyland's quest for eternal life from the Giants might be motivated by his dream to create an emotionally exact replica of human life in the form of a robot. So although Theron is far more advanced than David, she still has room for refinement. That her last name is Vickers is simply Weylan'ds way of giving her an additional level of identity separate from David's.
On an exegetical note -- whenever a magician says pay not attention over here, then there's something there that he really wants you to see, and it's a form of reverse psychology in the art of misdirection. Likewise, the text tried to dismiss the question of whether or not that she was an android in such an obvious way that it was like c'mon 97% of what I have seen codes her as an android, and you want me to place that 3% in the form of dialogue over what my eyes have seen? I'm sorry, people lie with their words all the time; I will trust my eyes.
I don't buy Lindelof's answer. Scott supercede's Lindelof as a director. The history of his work indicates that Meredith is an android. He codes her as such, frames her as such, has her walk and talk and posture as such. She moves silently as such. She could be the Terminatrix. If she were definitely human, than ambiguity would not be necessary. If she were android, ambiguity is understandable. I think Scott is smarter than that. So my answer is yes, she is an android. Until Scott himself says 'no.' If she is not an android, then I will be the first to admit that I was wrong. But I don't see why a smart director allows for that level of ambiguity. I think she is in such denial of her robotic nature that she needs to prove her humanity. Having sex does not mean she is not an android. Androids have simulated sex in Scott's films before. And David could be the android that does his physical (dark bidding), and Meredith could be the one that does his corporate bidding. He can use them as different aspects of his will seeing as how a man with secrets like himself can't trust anything he can't control.