Several others have reported being happy with the 
Ortlieb E-Mate pannier. It is specifically designed to carry a spare battery.
Personally I had a pair of 
Ortleib Back Roller panniers that I was very happy with so I just kept using them on the new ebike.  To carry a spare battery (that I borrow from my wife's ebike) I line the pannier with closed cell foam and velcro extra foam to the battery and slide it into place.  It's been working very well.