I wouldn't be surprised if you also found yourself confused by the NY Transit Museum. The directions say it's on the corner of Boerum Pl and Schermerhorn St, and the uninitiated could easily overlook the appropriateness of the museum being inside a decommissioned subway station. The seemingly misplaced subway entrance descending from the sidewalk is where you want to go. You can blame your befuddlement on a heat index near 105º if it helps.
Once inside, it's best to move quickly through the word-heavy history section and the electricity exhibit since these areas are not air-conditioned. There's a back area that is deliciously cool, though it's mostly "stuff for kids to play with," namely the front parts of buses with steering wheels to turn. If this all seems a bit disappointing, you'll be happy to find another, well-ventilated, level below: the still-operational tracks and signal room of the station, lined with an array of old subway cars.
Spend some time with an Art Deco era Bluebird (forebear of the Redbird), marvel at the comfort of wicker-covered seats, and feel the strange tug of contemporary recognition in a car with a map dated July 2009. It's worth a visit for any subway aficionado, though perhaps not at the height of summer when stagnant air will make the heat more apparent.