(I realize it's an old thread, but I've encountered a similar observation and rather than starting a new thread...)
I've noticed this problem for some time as well, although performance is generally still good enough to be manageable.
For the following, please note that I've typically found that running unlimited frames with vsync on gives me the best performance - so my goal is generally a smooth 30 fps from the virtual cockpit.
Last night, I installed a new GPU and my usual go-to for FPS and smoothness testing is KJFK - due to it being a combination of one of (if not the) highest scenery loads I own and being my most-used airport (about 1 in every 5 airliner flights to-date). Performance was generally very good, except when the terminals were in view - and it doesn't seem to matter what the heading is; whether the Manhattan skyline is in view or not. I long ago came to the conclusion that there was something in the terminal "infield" area causing a performance loss, but accepted it as there are many other add-on airports from various developers that seem to suffer similarly (FlyTampa KBOS is another good example - which is next on my list to look at with the new GPU).
It's also worth noting that I have Drzewiecki Design NYC (lite texture option) loaded - the default scenery must be horribly optimized because I don't notice any appreciable performance dip (aside from loading times/stutters) between the two, despite the DD version being at least a million times better.
In any event, I also came to a conclusion that the animated vehicles might have something to do with it. I did a flight into KJFK last night from the south, getting a steady 25 FPS or so between waypoints CAMRN and ASALT (heading straight towards Manhattan), with some momentary FPS dips as the DD scenery loaded. Proceeding from ASALT and onto the Parkway Visual to Rwy 13L, during the turn towards the runway with some of the expected stuttering as the airport assets loaded and after landing and roll-out, generally holding around 22 FPS. Parked at gate 507 (which faces roughly north), if I looked to the right I get a steady 28-30 fps. Looking forward, about 25. Looking left (towards the terminal "infield"), 17-22. FPS then increases the farther left (back) in the cockpit you look. (From this position, the Manhattan skyline is somewhere between left and ahead.)
However, pause the sim, and FPS pegs at 30. Unpause, and it dips back down as low as 17 FPS. In the past I've found FPS to rise somewhat during pause, but not usually that substantially! If I pull sliders back to the left (scenery complexity, water detail, special effects - autogen was already "low"), it'll improve only to about 19 FPS. Looking at the KJFK file structure and not seeing a clear way to disable those animated vehicles, I wasn't able to test my theory.
While I would like to pull those FPS closer to, say, 25, it does generally perform smooth enough. While I would like a way to disable those vehicles (if only just to test my theory), I'm content to wait for KJFK v3 if necessary, which I'm sure will contain a host of improvements.