Baking soda, as suggested above if your first step. If that doesn't work then a dilute solution of bleach mixed with water will kill any mold or bacteria. If you are squeamish about the bleach consider that the tablets sold to clean a camelback pouch contain bleach. Remember to rinse thoroughly if you use a mild bleach solution If bleach is not an option for you then buy a new bottle.
I use a lot of nalgene bottles and there is a point of no return where all the cleaning will not remove the odors, time for a new bottle.