Can you really say they focus on native species when they are going as broad as "The Americas"?
Yeah, for instance I've been to a lot of zoos that focus entirely on species native to the Earth. In that regards, everything is a native species!
If we want to look at "native species" through a more constrained lens, however, while in recent years they've deviated from their native routes, Buttonwood Park Zoo remains a good example of this as well. While they sadly no longer have black bears, their native New England collection still contains all three native felids, north american river otters, beavers, white-tailed deer, bald eagles, coyotes, harbor seals, sandhill cranes, and some of the zoo's waterfowl. Many of the zoo's farmyard species are also local heritage breeds. Historically, the zoo also had a number of shorebirds and fish from the local region, but many of these were eliminated to make way for the Rainforests exhibit.
New England Aquarium also has a few nice exhibits focusing on species native to the waters off the New England coast, and Boston Museum of Science has a nice area called "New England Climate Stories" that features blue jays, eastern screech owls, and some herps, fish, and inverts native to New England, along with some interpretive stations about climate.