Batman '89 was filmed at Pinewood Studios in London on a Backlot, and "Returns" was shot at both Warner Bros. and Universal Studios/Backlots in Burbank...so both of Burton's Gothams were entirely fabricated.
"Batman Forever" and "Batman & Robin" had segments of their Gotham's shot in both New York and Los Angeles, with some Studio/Backlot work to fill in gaps.
"Begins" and "TDK" had their Gotham's primarily shot in Chicago with additional shooting in the Cardington Hangar outside of London for locations such as the Narrows.
As far as picking an actual urban metropolitian city that feels like Gotham City, you really can't. Picking a real world city would either be based on the film versions, which are obvious...or the comic version, which is so over the top Gothic that it can't be pinpointed to just one city.
As far as a flesh and blood Gotham is concerned, since the city itself is such a caricature that it could never be real...I'd have to pick the one that visually looks the most like Gotham...one that would've HAD to have been replicated, which really only boils my choices to Burton's Gothams...and I would say the Gotham represented in B89 is as close to a flesh and blood, tride and true "Gotham City" as you could ever get.
And that said...I can't choose a real world city that could best substitute for Gotham...
CFE