John is freer than a World State citizen because he is capable of feeling a full range of emotions, including sadness. He doesn't just pop a pill the moment he starts feeling anxious. Because he is able to feel all his emotions deeply, he is free to intensely love the few individuals he feels close to, such as his mother, Linda, and to mourn for them when they die. He has also been exposed to literature and religion in a real way, reading Shakespeare and growing up in a religious tradition that is a hybrid of Christianity and Native culture. He has been allowed to feel pain and suffering and some of the magnificence of loving deeply. These are precisely the experiences that have been excised from the World State in favor of security, stability, social harmony, and a superficial happiness based on stunting and chaining the human spirit.

John, however, can be as much a victim of his own social conditioning as any member of the World State, especially in terms of sexual mores. He is as judgmental and unable to understand Lenina's free sexual giving as she is to understand why he would think she is a whore and a strumpet for sleeping with multiple men. He has rigid notions of fidelity and how dying should be handled. He is so unable to navigate the shock of his cultural encounter with the "brave new world" that he dies by suicide. Death is a form of freedom, arguably, but it is not the best for a young man with much to offer the world.

This question, like so many others, hinges on what "freer" means.  If you are a determinist/behaviorist, perhaps there is no such thing as freedom, so the question is irrelevant.  You might want to read B.F. Skinner's "Beyond Freedom and Dignity."

To my way of thinking, John is freer because he is aware of a larger range of options than the citizens of BNW.  They know only what they are programmed to know (although the Island indicates that the programming is less than perfect), so there is little to no chance that they are "free."  The real question is "Does John's wider knowledge really provide a wider range of choices than those of the citizenry?"  Does his upbringing give him a seeming range of choices that are easier for us to identify with, but give him a very small range of options because of his "formation"?

I know that he is the character that 'seems' freer, but I'm not sure that he really is.  I do suspect, however, that his version freedom is much more attractive to us than the alternative.

John was raised by his mother on an Indian reservation in New Mexico. His view of civilization is based on the stories his mother told him, but his view of what it means to be human is based on the Shakespearean plays he read, which was the only book he had access to while growing up. He is called the Savage because the world he grew up in is considered to be primitive by those in the civilized world. By most of our standards today, we would consider John to be freer than those in the civilized society of the brave new world. He's free to think and to have knowledge that those in civilized society don't have. He feels emotions, but the World Controllers have taken emotion, including pain, away from the people. They have taken truth, beauty, art, and God out of society, all the things that make people think and feel. John can't understand how anyone can live like this and knows he has no place in the brave new world. 

A fine question! I would say that yes, he is freer, but not completely free, and the reason is the second question you ask. The members of the state in Brave New World are consciously, methodically, and rationally conditioned. They are shaped by hypnotic slogans and drugs, as well as peer pressure, and the result markedly limits their thought. John, by contrast, is conditioned by the same sort of forces that shape you and me. He's shaped by prior generations, by the context into which he's born, the accident of family, and by literature. He is conditioned, but irregularly. This leaves gaps for pockets of freedom.

Is John the savage really more free than the other world state members? How is John conditioned in his own way?

      John the savage is more free than the other world state members because he was free born and has that which most in BNW do not have--freedom of choice. John the Savage has the choice to reject soma, the choice to read and enjoy Shakespeare, the choice to be happy or sad, the choice to experience and inflict pain on himself, and eventually, to take his own life. 

John is conditioned in his own way because he is a product of the savage reservation and only sees things through such a predispositional "lense." Depending on our backgrounds and upbringing, we cannot escape being "conditioned" in a certain way. So John is conditioned to feel, to suffer, to think for himself, and to choose simply because he was born and raised on the savage reservation. 

Is John really more free than the World State members in Brave New World? How is he conditioned in his own way?

The people outside the reservation have been conditioned from a young age by science, which has taken the place of conventional parenting.  However, someone who does have a parent can certainly be conditioned.  Ask yourself, "How does Linda's influence (her words, actions, life) form John's thoughts about the world?  How do Linda and her life have a hand in forming his fears, hopes, likes, and dislikes?  You can also ask yourself about others on the reservation.  How do Pope and Mitsima "condition" John to perceive the world?  What about his treatment at the hands of those on the reservation?  How does his conditioning within the reservation actually lead to a lack of freedom/decision when he leaves the reservation?