The Lexus will be more reliable than the BMW no question. How much more so depends on the exact model of X3 you are thinking of.

Comfort?, well with the BMW, a lot will depend on the wheel/tyre combo. Massive alloys with ultra low profile tyres will be a detriment to ride comfort, noise levels, mpg (slightly) and of course will be more expensive to replace. No personal experience of either, and while I'm sure the Lexus will also be affected by the wheel/tyre combo, I'd be very surprised if the Lexus wasn't more comfortable and refined, as they don't have the baggage of all that 'ultimate driving machine' nonsense to contend with.

How nice either would be to drive will depend how you drive. The BMW will be sportier and more responsive to fit with the image. The Lexus much more laid back, and wouldn't be much fun to drive hard as the hybrid drivetrain is much more suited to a more relaxed gait.

For me it would be the Lexus all day long.