In the UK there a of companies that specialise in this sort of small volume custom design and they can do custom embroidery and printing. Yeah, you pay extra for it but it isn't` super expensive. I don't know about the US, but seeing as you guys must have loads of sports teams and therefore a similar demand I'd be surprised if companies don't exist to meet this sort of demand in the US.
Whether companies likes this will work for you depends on what you're going to do with the hoodies. If they're just for you and you crew or a team than these guys are probably the way go for you. They are capable of quite a lot and are pretty flexible. E.g. our team tops have two base colours, embroidered crests on the chest, three large prints of sponsors logos (of different designs with multiple colours) on the front, sleeves and back. This isn't particularly unusual work for these sorts of companies. The price charged for our team hoodies was about the same price as hoodies in the uK from the likes of Aramda, 4FRNT etc... (their regular hoodies, not the technical ones water resistant or soft shell ones).
But if you're trying to do this to make money then the price of using these types of business is probably too high while and the volume they specialise in is too low so the margins on sales will be paper thin.