<p>I'm using NuSOAP on PHP 5.2.6 and I'm seeing that the max message size is only 1000 bytes (which makes it tough to do anything meaningful). Is this set in the endpoint's WSDL or is this something I can configure in NuSOAP?</p>

I am only passingly-familiar with PHP, and have never used the NuSOAP package at all. However, a SOAP message's size should only be limited by the transport medium. In the case of HTTP, it should be pretty much unbounded (the limitation of 16384 bytes in form POST requests isn't due to SOAP, it's from browser limitations (which may actually not exist anymore, but I don't know for certain)).
I would recommend finding a contact address for the authors/maintainers of NuSOAP and ask them directly. Unless there's something in the WSDL (and I don't recall anything in the WSDL spec that would limit a whole message-body-size... individual parameters (via XML Schema facets), but not the overall body), then the limitation would seem to be in the toolkit.