金:
A general term for money in specific situations, not necessarily in exchange for something, might even not cost. It's a fallback option when none of the rest could apply.
保証金, 入学金, お祝い金, 所持金, 補助金, 契約金, 敷金, 賠償金
~料:
Charge or fee for activities done, typically charged by organizations with a predetermined amount of money.
授業料, 手数料, 送料, 使用料, サービス料, 通行料, キャンセル料
~代:
Price or charge in exchange for concrete (doesn't mean tangible) items. Most widely used.
食事代, 飲み代, タバコ代, バス代, バイト代, 電気代, 地代, 修理代
~費:
Overall expenses for specific activities, not used for detailed items.
医療費, 交通費, 学費, 生活費, 食費, 参加費