Drain Bocconcini and dry thoroughly with paper towel.
In a large dish, combine flour, salt and black pepper.
In a bowl, whisk eggs with a fork.
In another bowl, mix bread crumbs, lemon zest, oregano, thyme and garlic until fully combined.
Coat a Bocconcini ball in the flour, then in the egg, and finally, in the bread crumbs. Coat once more in egg and bread crumbs. Place on a dish and repeat with remaining Bocconcini. Place the prepared Bocconcini in the freezer for 20 minutes.
Pour canola oil into a deep saucepan, creating a 2.5 cm (1 inch) layer. Heat on medium until the oil reaches 190 °C (375 °F). Using a slotted spoon, drop 5 prepared Bocconcini balls into the oil. Fry the Bocconcini for 15-20 seconds, turning frequently, until golden. Transfer onto a plate lined with paper towel. Repeat with the remaining Bocconcini, making sure that the oil stays at the proper temperature (adjust heat if needed).
Season the fried Bocconcini with sea salt and serve hot with tomato sauce and lemon wedges.