Sistema who manufacture some of the most popular bottles recommend that after use you remove the cap from the bottle, extend the pop up sipper to the open position and put the top either in the dishwasher or hand wash and then place in water for five minutes with a sterilising solution.
Under normal use this should be sufficient to clean the cap. They do however have videos available detailing how to fully clean the bottles which I have included below.
Twist N Sip Bottle Cap Cleaning Instructions Video from Sistema Plastics on Vimeo.
Davina Bottle Cleaning Caps instructions from Sistema Plastics on Vimeo.
Wave and Gripper Bottle Cap Cleaning Instructions from Sistema Plastics on Vimeo.
Another popular brand is Munchkin, so I have included the video for cleaning their Miracle Cups.
It is recommended that plastic drink bottles that are continually in use should be replaced every 12 months.