Have you test-driven both of them ? I suggest you try 4.8 X5 and X6 (5.0 and 3.5).

If you dont have kids, X6 is probably safe choice cargo space wise, but you should read cmyX6go review - lack of rear wiper, some rear view obstructions, etc and see if they make a difference for you.

As for the oversized parking extra fees in NYC - some places charge, and some dont. I drive-in in NYC quite often, and know a few places where they dont charge those fees. But in any, X5 and X6 are the same when it comes to paying the fee.

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His : 2013 X5 3.5d Deep Sea Blue/Black/Aluminum with ALL packages, 20" 214"s, running boards, Adaptive Drive, Spare Tire, BMW Apps
On Order : 2016 X3 3.5 MSport Silver/Mocha with DHP, CW, Prem, Tech, DA, Lighting

Hers : 2015 328xi MSport Silver/Red

Prior:
2008 X5 4.8
2011 X5 3.5d
2010 335 xDrive
2013 335 xDrive