Route 8 (Murraile Coast): The only in-game location where you can find Shellder. Naturally it's a good idea to farm Pearls and Big Pearls here. You can find Shellders here by using your Good Rod and the rarer Cloysters as well with your Super Rod.
Friend Safari: Ice type safaris with Cloysters are also good places to farm Pearls andBig Pearls. It's a 33.33% chance to find a random encounter Cloyster here, but on the plus side you don't have to fish.
Other than these locations, Cloysters and Shellders, your main means of acquiring Pearls, are found nowhere. So these are.pretty much your only locations.
Hope I helped!