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Agree, for the price, Sugar Sweet Sunshine are the obvious pick. They offer a good assortment of child friendly flavors too.
Eleni's discounts cupcakes after 5pm or something like that. Pre-ordering is probably the better idea however.
I would also think that when you buy in bulk you can get a reduced price. I'd try Georgetown or Billy's for a larger order.
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By happy coincidence, some of the best cupcakes in the city also happen to be some of the cheapest:
http://www.sugarsweetsunshine.com/
(Note, I can't vouch for their $1 mini cupcakes, but their regular cupcakes are among my favorite.)