Could it also be that the dock is blocking the Bluetooth signal enough to make it drop out sometimes/past certain distances? And it works in tabletop as the tablet is out in the open and not obstructed by the dock?
EDIT: Lol, did read the above post first.
I think it'd be less to do with the Dock itself, and more to do with the JoyCon. The Pro Controller likely uses the same kind of technology, but has no problems in any mode.
Essentially, the JoyCon have three configurations;
Attached to the Switch (Handheld)
Disconnected from the Switch (Tabletop)
Disconnected from the Switch (TV Mode/Docked).
From what I can see, it's only the last configuration that's having trouble with signal. I'm leaning towards the JoyCon entering into a low power Bluetooth mode when the Switch is docked.