I received my core set last night. When I was taking a look through the cards, I noticed that some refer to tokens that are not included in the box, e.g. Tears of Lys refers to poison tokens, Jorah Mormont refers to betrayal tokens. Does this mean that the mechanics won't become active until a later boxed expansion or can I proxy the tokens in the meantime?

There are generic tokens (with a different color on each side) that you can use as poison tokens, betrayal tokens, stand tokens, or any other type of tokens that could be created in the future.

There is a detailed description of the generic "influence tokens" that do come in the box on p. 10 of the RRG.