With respect to Wonders, I go with the assumption, based on historical evidence, that they were income producers long before long before they are 1,000 years old. Therefore, I give most of them, specifically the ones with buildings associated with them, the +1 commerce bonus that comes with the Colossus. My basis for this follows. I have also increased the cost of some of the Wonders to reflect the higher value.
If you want to get a quick idea, take a long at the events recorded in the book of Romans about Paul's visit to Ephesus, site of the Temple of Artemis/Diana, and how much money the city was making off of it at that time. Similarly, to consult the Oracle at Delphi cost cold, hard cash, making the treasury at Delphi quite rich, along with being an great place for archaeologists. The Great Lighthouse helped to make Alexandria the premier port in the Ancient World, while the Great Library developed a wide range of sophisticated hot-air and water power gadgets for temples to use to extract donations from worshipers, include a coin-operated holy water dispenser and coin-operated prayer wheel. The Great Library was more a cross of an information bank, an engineering school, and a research and development lab.
Remember, there was a reason why these things were built, and in many cases, one of the reasons was a commercial one. The Pyramids were built as tombs, but the Egyptians were taking visitors on tours of them for an extremely long period of time, based on the account in Herodotus. The Hanging Gardens are probably the main exception to this commercial emphasis, but given the writings of the Greeks, probably had similar effects.