Toysrus has the most selection
Target also has a lot of stuff, usually a tad cheaper but often out of stock (probably depends on which Target)
Kroeger has those GIANT ponies - and other stuffs - cheaper than above.
HotTopic has the Funko ponies, and general merch (like t-shirts and socks and necklaces and things)
Kmart and Walmart usually always have pony stuff too. Kmart is cheap but disorganized, Walmart is the evil empire so I try not to support them (but ponies are cheap there too)