Immigration/Customs will indeed need to be cleared at the initial point of entry. Domestic flights (i.e. EWR-IAH) arrive in the domestic arrivals section, and "hiding" on the plane is not possible.

That being said, the EWR folks have been very nice to me overall. And it's usually well staffed and waiting time is minimal, compared to say IAD. Make sure you fill out those forms in advance though.