Once you remove the black plastic cover on the passenger side to get to the air filter, just look around its plastic housing. Normally the rubber that seals the filters housing to the car stops working and when it rain it poors behind the filter and around the plasting housing. What a lot of people have done is clean and cake on silicon.
There are also some water draining holes on each side of the car under this plastic area. Check to make sure those are not filled up with trash. If the water level fills up in this area it will leak back into car.
Also while the cover is off take a look at the plastic tabs that hold the window in place. Sometimes water leaks into those holes. Just cake it all up and let it dry for a few days then run the spinkler over the car for a few hours or wait till it rains again..lol
