Most of the small towers are FAA and so you would apply to the FAA under their normal hiring bids. You don't apply for a specific facility, they give you a list of options to pick from. Some others are Federal Contract Towers and are operated by various contracting companies such as Midwest, SERCO, and RVA. To apply for those you apply through the companies website. Generally speaking you'll need at least a few years of prior ATC experience with a CTO to be hired by the contract company as they don't have the desire or need to train someone from scratch.