Which Bus Station is closer to Chapala? Guadalajara or Zapopan
It would definitely be Guadalajara, but if you call the bus company ask them if they don´t stop at the airport. Some buses do that, if that is the case, then getting off at the airport is your best option.
There is one huge bus station that will connect to Chapala, it is called Central Nueva even if it is 40 yr old. /www.reservamos.mx/central-autobuses/t-guadalajara-central-nueva