How do you put a Stained Glass Block on an Armor Stand's Head?

The Equipment list was updated in 1.9 to ArmorItems.

Your list also contains 4 empty brackets and then the item bracket. This is too many. The head slot is the 4th bracket set. This is probably because you were working with a pre 1.9 command to start with.

You are also missing Count to specify quantity.

I also specified data types by following the number value by the proper letter.

These commands have been tested and work properly in 1.12.2:

/entitydata @e[type=armor_stand,r=1] {Invisible:1b,ArmorItems:[{},{},{},{id:"minecraft:stained_glass",Damage:14b,Count:1b}]}

/summon armor_stand ~ ~ ~ {Invisible:1b,ArmorItems:[{},{},{},{id:"minecraft:stained_glass",Damage:14b,Count:1b}]}