Well, obviously Harvard. Their Semitic museum normally funds a number of different projects. Right now, they have been re-digging in Ashkelon with the Leon Levy expedition. It's co-run by Dan Masters (from Wheaton) and Lawrence Stager.
UT-Austin is a new up and coming program. Both L. Michael White and Steve Friesen in their AMR concentration are pretty heavily involved in digs every summer, and I'd keep an eye for this school in years to come for sure.
Other than that, I could almost gurantee that any top notch program (Duke, Emory, UChicago, etc.) will have connections and ties to excavators.