Not in 1.8
While your command works in principle, as of 1.8.8 the game is unable to render many items in the head slot, including flower pots.
Kind of in 1.9
However, as part of the new Snapshots/Upcoming version 1.9, Mojang Dev Grum (Erik Broes) has worked on rendering all item on entities and published a world showing off zombies wearing items, including flower pots:
Sadly, this will still only display the item as if lying on the ground, rather than the rendered version of a flower pot (the tile entity), and it will be placed at the back of the head (like the flowers in the screenshot above), meaning it will float above the armor stand.
Also note that the Equipment
tag was split into ArmorItems
(Feet, Legs, Chest, Head) and HandItems
(Mainhand, Offhand) to accomodate dual-wielding, so the command would be
/summon ArmorStand ~ ~ ~ {ArmorItems:[{},{},{},{id:"flower_pot",Count:1}]}